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FSL List Archives2024-03-19T12:04:08ZPowered by L-Soft's LISTSERV mailing list manager
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http://www.lsoft.com/images/listserv_small.gifRe: Discrepancies between timepoints in featquery outputs.
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;e9e6150.2403
Dear Alex,<br>I’m not sure there’s any actual _problem_ here - I’m guessing the scan has a shorter TR, so given the event timings, some overlap is possible..<br><br>Kind Regards<br>Matthew
2024-03-19T12:03:58+00:00Matthew Websterhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;e9e6150.2403Re: Discrepancies between timepoints in featquery outputs.
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;700d82e0.2403
Dear Matthew,<br>You are right about the output of peristimulus (ps) time series. What could be causing this? Where file should I examine?<br>Thank you.<br><br>Best,<br>Alex
2024-03-19T09:39:59+00:00Sheng Yanghttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;700d82e0.2403resting state design to use for fsl_glm
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;4cc8c347.2403
Hello FSL users,<br><br>I am trying to regress out specific confounders from fmriprep output in CLI and compare the effect of removing each set of components on some post-processing I do.<br>I have my selected confounders copied in columns as txt file and converted to mat using<br>Text2Vest design.txt design.mat<br>and ran:<br><br>fsl_glm -i sub-x_ses-1A_task-rest_dir-AP_run-1_space-T1w_desc-preproc_bold.nii.gz -d design.mat --out_res=denoised_name.nii [...]
2024-03-18T22:23:13+00:00Taha Gholipourhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;4cc8c347.2403Re: Discrepancies between timepoints in featquery outputs.
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;ee36cbe0.2403
Dear Alex,<br>I suspect this is due to the end of one peri-stimulus period merging into the start of the next - you can check the ps timeseries outputs for this - the last few rows of one period will be identical to the starting rows of the next.<br><br>Hope this helps,<br>Kind Regards<br>Matthew
2024-03-18T20:28:42+00:00Matthew Websterhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;ee36cbe0.2403Re: DOF cannot be zero or negative!
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;71923425.2403
Hi Roberto,<br>You could run the first two-stages of dual_regression on a single subject ( as obviously no cross-subject modelling can take place ) but you would need to perform any inference yourself on ( e.g ) the z-stat outputs. I’m not sure how useful this would be though as your inference would be limited to that subject - potentially only interesting in cases of unusual pathology or similar? [...]
2024-03-18T17:24:05+00:00Matthew Websterhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;71923425.2403Re: randomise with several voxel-dependent EVs
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;312e02c2.2403
Dear Roman,<br>If I understand correctly, each subject can have missing values for one or more of the data and the two voxelwise EVs. In general, it’s probably worth adding a column of ones to the design as a “normal” EV ( to model the overall mean ). For the missing values, one approach might be to create a single exclusion EV ( i.e. the binary inverse of each subject's overall validity ) which will fully regress out a subject’s data when 1. Randomise will remove null EVs when partitioning the design so all-zero columns will be removed from the [...]
2024-03-18T17:05:46+00:00Matthew Websterhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;312e02c2.2403Re: randomise with several voxel-dependent EVs
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;312e02c2.2403
Dear Roman,<br>If I understand correctly, each subject can have missing values for one or more of the data and the two voxelwise EVs. In general, it’s probably worth adding a column of ones to the design as a “normal” EV ( to model the overall mean ). For the missing values, one approach might be to create a single exclusion EV ( i.e. the binary inverse of each subject's overall validity ) which will fully regress out a subject’s data when 1. Randomise will remove null EVs when partitioning the design so all-zero columns will be removed from the [...]
2024-03-18T17:05:46+00:00Matthew Websterhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;312e02c2.2403Re: xtract_blueprint unusual output
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;d5aac2e9.2403
Hi Estephan,<br><br>That target set-up sounds like it should be ok.<br><br>For the medial wall ROI, it sounds like you have 1s for the medial wall and zeros for the cortex? The ROI expects 1s for regions you want to keep (i.e. cortex) and 0s for regions you want to discard (i.e. the medial wall). If you have the output from the HCP processing pipeline, you can use the atlasroi files. [...]
2024-03-18T16:59:20+00:00Shaun Warringtonhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;d5aac2e9.2403xtract_blueprint unusual output
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;637cdd80.2403
Hi, I'm trying to run xtract_blueprint using my dataset and saw some unusual results. I have 52 participants with HCP-like imaging protocol that was pre-processed using the HCP pipelines. I have two questions:<br>- For the "-target" parameter entered, I used the "wm.mgz" file output from the freesurfer stream, and converted it to NIFTI and thresholded it to only include the white matter. Does this sound correct?<br>- More importantly, I included the "-rois" parameter with the left and right medial walls to exclude them from seeding as recommended. However the resulting output file "BP.LR.dscalar.nii" only showed results over the [...]
2024-03-18T16:46:43+00:00Estephan J. Moana-Filhohttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;637cdd80.2403Clinical Research Coordinator Position at Duke University - Adcock Lab
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;880b0dbd.2403
The *Motivated Memory Laboratory* <https://www.adcocklab.org/> in the<br>Center for Cognitive Neuroscience and Department of Psychiatry at Duke<br>University is seeking a full-time *Clinical Research Coordinator* with<br>strong interest in understanding how motivation shapes human experience to<br>work on an NIH-funded project (*PI: R. Alison Adcock*). This project aims<br>to uncover the neural mechanisms of motivation and its regulation using<br>fMRI neurofeedback and advanced statistical modeling. [...]
2024-03-15T17:54:43-04:00Jia-Hou, Pohhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;880b0dbd.2403Postdoctoral Position at Duke University - Adcock Lab
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;abb6ba1b.2403
*Postdoctoral Researcher in the Cognitive Neuroscience of Motivation and<br>Memory at Duke University*<br>The *Motivated Memory Laboratory* <https://www.adcocklab.org/> in the<br>Center for Cognitive Neuroscience and Department of Psychiatry at Duke<br>University is seeking a full-time Cognitive Neuroscience *Postdoctoral<br>Researcher* with strong interest in understanding how motivation shapes<br>human experience to join the team and lead an NIH-funded project (*PI: R.<br>Alison Adcock*). This project aims to uncover the neural mechanisms of<br>motivation and its regulation using fMRI neurofeedback and advanced<br>statistical modeling. [...]
2024-03-15T17:53:54-04:00Jia-Hou, Pohhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;abb6ba1b.2403Re: Breaking up large clusters
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;f28df4a7.2403
Sorry for being unclear - I'm not using cluster size inference, but rather randomise with tfce. My understanding is that the *_tfce_corrp_tstat* output images are voxelwise corrected for multiple comparisons - is that incorrect? If not, the issue I'm having is not with the correction itself, but rather how I can interrogate the findings (see below). [...]
2024-03-15T18:33:31+00:00Jeffrey Spielberghttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;f28df4a7.2403Re: FDT registration
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;afbb6759.2403
Dear Antonio,<br><br>what are the types of images in which FNIRT is used instead of FLIRT?<br>An example is the istance of subjects with atrophy.<br><br>we recommend using FNIRT instead if FLIRT when registering individual subjects to a template in standard space (for example MNI152). It is able to achieve a much closer alignment compared to an affine transform such as FLIRT. Only for very poor quality data would we recommend FLIRT instead of FNIRT for that purpose.<br>But note that we recommend initiating FNIRT with an affine transform from FLIRT, as it is more robust to brains that are [...]
2024-03-15T18:06:34+00:00Jesper Anderssonhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;afbb6759.2403Re: FIX installation failing
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;a30a610f.2403
Hi Marie,<br>Everything should already be in place for the script to run, the training data names are slightly different to the legacy version ( you can run fix without any options to see the available models ).<br><br>Kind Regards<br>Matthew
2024-03-15T16:40:04+00:00Matthew Websterhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;a30a610f.2403Re: stand-alone TFCE
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;7dc5a024.2403
Thank you, Stephen !<br><br>Roman
2024-03-15T14:47:14+00:00Roman Fleysherhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;7dc5a024.2403FDT registration
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;a73305bf.2403
Dear FSL experts,<br><br>what are the types of images in which FNIRT is used instead of FLIRT?<br>An example is the istance of subjects with atrophy.<br><br>Thank you in advance,<br><br>Antonio
2024-03-15T09:50:41+00:00Antonio Drhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;a73305bf.2403Regarding the statistical analysis in FSL
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;37616c00.2403
Hello,<br><br>I have already computed the z-transformed R map for my connectivity analysis. I would like to know if I can use FSL to do the following statistical analyis, for example the paired t test by comparing the connectivity map between two different clinical conditions. If yes, could you please give me a demo script ? Also i would like to incorporate some clinical variables as covariates. Can fsl achieve this? [...]
2024-03-15T09:17:21+00:00Zhengyu Linhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;37616c00.2403Re: stand-alone TFCE
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;e5e19c5f.2403
Hi Tfce doesn’t take in dof so if you need to make that consistent across voxels you could first convert t to z.<br>Cheers.<br><br>Sent from Outlook for iOS<https://aka.ms/o0ukef>
2024-03-15T00:59:54+00:00Stephen Smithhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;e5e19c5f.2403Re: stand-alone TFCE
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;49869561.2403
Thank you, Stephen ! That would work.<br><br>How do I supply degrees of freedom to fslmaths associated with map of t-statistics?<br><br>Roman
2024-03-15T00:43:29+00:00Roman Fleysherhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;49869561.2403Re: Timing file text (EV) for FEAT analysis
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;80609af5.2403
Seems like the INPUT field didn't update from my bash script's FEAT call. Fixed the error when it was changed to reflect on the new fsf file(s).<br><br>Thanks,<br>Suja
2024-03-14T23:06:36+00:00Suja Reddyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;80609af5.2403Re: stand-alone TFCE
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;149e2b78.2403
Hi - you can't get TFCE-related p-values of course, but you can feed voxelwise tstats into fslmaths with the -tfce option.<br>Cheers.<br><br>On 14 Mar 2024, at 22:40, Roman Fleysher <000091d32badfb02-dmarc-request@JISCMAIL.AC.UK> wrote:<br><br>Dear FSL developers and Users,<br><br>If I have a map of p-value or a t-statistics, is it possible to carry out Threshold-Free Cluster Enhancement, i.e. without running randomise? So to speak, TFCE in a stand-alone way? From what I understand, logically it should be possible but I may be wrong. [...]
2024-03-14T22:43:01+00:00Stephen Smithhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;149e2b78.2403stand-alone TFCE
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;efb1ad50.2403
Dear FSL developers and Users,<br><br>If I have a map of p-value or a t-statistics, is it possible to carry out Threshold-Free Cluster Enhancement, i.e. without running randomise? So to speak, TFCE in a stand-alone way? From what I understand, logically it should be possible but I may be wrong.<br><br>Thank you, [...]
2024-03-14T22:40:28+00:00Roman Fleysherhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;efb1ad50.2403Timing file text (EV) for FEAT analysis
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;54b85246.2403
Full message available at: <a href="https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;54b85246.2403">Timing file text (EV) for FEAT analysis</a>2024-03-14T19:11:22+00:00Suja Reddyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;54b85246.2403FSL Course 2024 - Registration Open!
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;2c674722.2403
Dear all,<br>Registration is still open for FSL Course 2024, which will be held in-person June 17th – 21st in Osaka, Japan, co-hosted by the Riken Center for Biosystems Dynamics Research. You can find details and registration info here:<br>https://open.win.ox.ac.uk/pages/fslcourse/website/upcoming.html<br><br>Spots on the course are limited and will be allocated on a first-come-first-served basis. Please register early to avoid disappointment. [...]
2024-03-14T16:29:23+00:00Rezvan Farahibozorghttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;2c674722.2403Re: FIX installation failing
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;df0ca564.2403
Hi Matthew,<br><br>Thank you for your response.<br><br>Could you please clarify what I need to do in order to use the fix script that is included in $FSLDIR/bin? Is there anything I need to compile before calling the script to clean the data?<br><br>Thanks,<br><br>Marie<br><br>Marie-Eve Hoeppli, Ph.D.<br>Research Associate<br><br>Center for Understanding Pediatric Pain<br>Department of Behavioral Medicine and Clinical Psychology<br>Cincinnati Children’s Hospital<br>3333 Burnet Ave, MLC 7020<br>Cincinnati, OH, 45229-3026 [...]
2024-03-14T14:15:44+00:00Marie-Eve Hoepplihttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;df0ca564.2403Re: Breaking up large clusters
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;16358aeb.2403
You could also use standardized effect size benchmarks<br><br>On Thu, Mar 14, 2024, 06:46 Thomas Nichols <<br>0000c0d4b0357566-dmarc-request@jiscmail.ac.uk> wrote:<br><br>> Dear Jeffrey,<br>><br>> To add to Matthew's reply, we use cluster size inference to maximize power<br>> with very weak signals. It sounds like you have quite strong signals, so<br>> my question is: Why are you using cluster size inference? With strong<br>> signals you can afford to use (more spatially-specific) voxel-wise<br>> inference.<br>><br>> -Tom<br>><br>> On Wed, 13 Mar 2024 at 17:52, Jeffrey Spielberg <jspielb2@gmail.com><br>> wrote:<br>><br>>> Does anyone know of a [...]
2024-03-14T06:52:43-04:00Alexander Joseph Shackmanhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;16358aeb.2403Re: Breaking up large clusters
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;cbf718e5.2403
Dear Jeffrey,<br><br>To add to Matthew's reply, we use cluster size inference to maximize power<br>with very weak signals. It sounds like you have quite strong signals, so<br>my question is: Why are you using cluster size inference? With strong<br>signals you can afford to use (more spatially-specific) voxel-wise<br>inference.<br><br>-Tom<br><br>On Wed, 13 Mar 2024 at 17:52, Jeffrey Spielberg <jspielb2@gmail.com> wrote: [...]
2024-03-14T10:45:53+00:00Thomas Nicholshttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;cbf718e5.2403Exciting Postdoctoral Position Available at UCSF's Tee Lab - Neuroimaging Research
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;c0ea8175.2403
We are thrilled to announce an opening for a Postdoctoral Position at the Tee Lab, Department of Neurology, University of California, San Francisco (UCSF). This is a unique opportunity for a passionate researcher to contribute to groundbreaking work in the field of neuroimaging and neurodegenerative diseases.<br><br>Job Summary: The selected candidate will participate in projects that focus on establishing MRI protocols with cutting-edge methodologies and applying neuroimaging techniques, such as tractography, graph theory analysis, and machine learning algorithms. Our focus spans a range of neurodegenerative diseases, including Alzheimer’s disease, primary progressive aphasia, and frontotemporal dementia, particularly in the context of [...]
2024-03-13T23:38:04+00:00Chen Yuhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;c0ea8175.2403FSLeyes render error
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;7e01b5f5.2403
Hi there - I'm trying to generate 3d renders using fsleyes command line tools but I'm getting the "unrecognized arguments" error. I've used the same command in my workflow previously and it used work without any issues. I tried the command with the version (v1.7) of fsleyes it worked with last time (a few months back) and also with the latest version but got the same error. [...]
2024-03-13T20:43:39+00:00SUBSCRIBE FSL Arshithahttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;7e01b5f5.2403Re: Breaking up large clusters
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;a9c466cf.2403
Hi Jeffrey,<br>300k voxels is certainly a very large cluster - I would potentially be worried about excluding modelling issues here - can you upload your design matrix and contrast ( and a brief description of the input data )?<br><br>Kind Regards<br>Matthew
2024-03-13T20:13:09+00:00Matthew Websterhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;a9c466cf.2403Fwd: The Open Science Room at OHBM
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;8591571b.2403
Forwarded at the request of Selma Lugtmeijer:<br>The Organization for Human Brain Mapping (OHBM) is excited to invite self-nominations for panelists, volunteers, and submissions for emergent sessions for the Open Science Room (OSR) at this year’s annual meeting in Seoul, Korea (June 23 - June 27, 2024).<br>Why Get Involved?<br>Panelists: Join one of our five panel discussions on critical open science topics, ranging from funding issues to the rise of crowdsourcing in brain mapping.<br>Emergent Sessions: Lead a spontaneous, hot-topic talk or panel—ideal for collaborative projects or discussing new developments.<br>Volunteers: Support the OSR and contribute to the success [...]
2024-03-13T18:33:05+00:00Matthew Websterhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;8591571b.2403Group feat error: tmpreport_poststats.html
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;e38d82c7.2403
I am getting an error when running group feat on the poststats side. The error is saying that it cannot find tmpreport_poststats.html (line 312 of feat). Has anyone encountered this and discovered a solution.<br><br>-Matt
2024-03-13T17:55:48+00:00Sherwood, Matthttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;e38d82c7.2403Breaking up large clusters
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;5163a47d.2403
Does anyone know of a principled way of breaking down large clusters into sub-clusters?<br><br>For example, I'm looking at very robust task effects for a paradigm my lab developed, and after running randomise (with tfce), I end up with a single cluster of over 300k voxels. I'd typically decompose the effects to see what conditions are driving the differences by taking the mean across the cluster, but that's pretty meaningless when the cluster is so large, as there may be key differences across different regions. [...]
2024-03-13T17:51:40+00:00Jeffrey Spielberghttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;5163a47d.2403GUI: cluster mass option
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;fa48e80e.2403
Dear FSL-experts,<br><br>we love FSL and are grateful that you put in so much hard work! Just a tiny request: in a future release, we would love to see the cluster mass option in the GUI.<br><br>Best,<br>Marvin
2024-03-13T17:39:06+00:00Marvin Meieringhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;fa48e80e.2403Re: FIX installation failing
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;97e75c3d.2403
Hi Marie,<br>I just checked the conda-channels and it looks like R3.4 is not available for ARM - as well as the compile issues using legacy FIX with a newer R will mean that the existing models won’t be usable. As you have already installed the latest version of FSL, I would strongly recommend trying pyfix first - there should already by a “legacy-compatible” fix script in $FSLDIR/bin and $FSLDIR/share/fsl/bin as well as ports of all the old FIX models. [...]
2024-03-13T17:15:17+00:00Matthew Websterhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;97e75c3d.2403Re: DOF cannot be zero or negative!
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;21a9f92b.2403
Hi Matthew<br><br>Thanks for all your help. I wanted to give an update. The problem was<br>occurring with certain images at the point when dual regression was<br>creating the binarised versions of the Tstd. Upon inspection, it seemed<br>that the problem was caused by those images having a strong signal coming<br>from outside the brain. Such as the eyes, where there might have been a<br>problem with pre-processing. When I applied a brain mask to the images<br>(standard MNI152, as provided by FSL), then dual regression worked! [...]
2024-03-13T16:23:47+00:00Roberto Dos Santoshttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;21a9f92b.2403UCSF Postdoctoral Fellowship Position
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;58e7ca07.2403
Dr. David Perry (https://perrylab.ucsf.edu/) is now inviting applications for a NIH-funded postdoctoral fellowship position in his lab at the University of California, San Francisco (UCSF) Memory and Aging Center. The goal of our lab’s research is to elucidate brain-behavior relationships in neurodegenerative disease in order to improve diagnostic certainty and identify therapeutic targets. [...]
2024-03-13T15:56:09+00:00Noah Crynshttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;58e7ca07.2403Re: FIX installation failing
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;8081df85.2403
Hi Matthew,<br><br>Thank you for all your advice.<br><br>I updated my FSL version and conda. Then I was able to install R and the required packages using the instructions you point me too.<br><br>I am having the following error when I try install_version(“mvtnorm”, version=“1.0-8”), as well as coin and party:<br><br>Error: Failed to install 'unknown package' from URL: [...]
2024-03-13T15:41:10+00:00Marie-Eve Hoepplihttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;8081df85.2403FSL window freezes post GLM design
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;4e2d1f8c.2403
Dear Saad<br><br>I am trying to run an analysis with 33 subjects having undergone two different tasks. When designing the full model using FULL MODEL SETUP in stats for higher level analysis, post all the 0's and 1's, when I press done, the FSL freezes and does not return the design window. I have had this for longest time and it works well when I have lesser inputs, for e.g, 20. I don't think this is any issue with my system as it has 32 cores, 64GB RAM and 2TB SSD to make it work. What can be done here? [...]
2024-03-13T15:25:43+00:00Divesh Thaploohttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;4e2d1f8c.2403Re: downloading FSL MRS tutorial data
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;25e2fe5b.2403
Hi Saad,<br><br>Thanks very much - used it and sorted now!<br><br>Sean
2024-03-13T14:56:36+00:00TAN, Sean (ROYAL PAPWORTH HOSPITAL NHS FOUNDATION TRUST)https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;25e2fe5b.2403Re: downloading FSL MRS tutorial data
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;dc4b8109.2403
Hi Sean<br><br>Have you tried the fsl_add_module command? If you have FSL installed, you can use this command and when prompted, choose the number that corresponds to the MRS data (#11).<br><br>Cheers<br>Saad<br><br>From: FSL - FMRIB's Software Library <FSL@JISCMAIL.AC.UK> on behalf of TAN, Sean (ROYAL PAPWORTH HOSPITAL NHS FOUNDATION TRUST) <0000672db0bb4617-dmarc-request@JISCMAIL.AC.UK><br>Date: Wednesday, 13 March 2024 at 14:44<br>To: FSL@JISCMAIL.AC.UK <FSL@JISCMAIL.AC.UK><br>Subject: [FSL] downloading FSL MRS tutorial data<br>Hi FSL team, [...]
2024-03-13T14:50:06+00:00Saad Jbabdihttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;dc4b8109.2403downloading FSL MRS tutorial data
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;d572903e.2403
Hi FSL team,<br><br>I am trying to download the fsl mrs tutorial data using the following commands that I have seen from https://open.win.ox.ac.uk/pages/fslcourse/website/downloads.html. As the fsl mrs course data was not explicitly mentioned I tired using the following command from my terminal<br><br>curl -L -# -O -C - https://fsl.fmrib.ox.ac.uk/fslcourse/downloads/fsl_mrs.tar.gz<br><br>However when i try to tar the .gz file that is downloaded it says tar: Error opening archive: Unrecognized archive format [...]
2024-03-13T14:43:38+00:00TAN, Sean (ROYAL PAPWORTH HOSPITAL NHS FOUNDATION TRUST)https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;d572903e.2403pnm_evs voxelwise EVs appear empty
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;a9077436.2403
Dear fsl community,<br><br>I have troubles creating physiological noise regressors recorded by biopack using pnm.<br>First, I still have the same trouble with running pnm from the command line as stated in the email below from the archive- the .txt file includes all files in that folder. Please could you confirm if the correct ev_list should be a list only including the ev_0*.nii.gz files created in the process, but not any of the .txt or .html files also in that folder?<br>Second, the ev_0*.nii.gz files created in the process are quite small (168 bytes) and appear to be all 0s [...]
2024-03-13T10:58:31+00:00Svenja Kuchenhoffhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;a9077436.2403Postdoctoral Position on PET and structural MRI/DTI at Brown University
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;6d6e21b7.2403
Position: Postdoctoral Position in Neuroimaging Research on Brain<br>Aging and Alzheimer’s disease<br><br>Area: Brain Aging and Alzheimer’s disease<br><br>Department: Department of Psychiatry and Human Behavior<br><br>Institution: Brown University<br><br>We are seeking a highly motivated postdoctoral researcher to lead an<br>NIH-funded project in the Laboratory for Cognitive and Translational<br>Neuroscience (Director: Dr. Hwamee Oh) at Brown University. The<br>project is to use amyloid and tau PET and structural MRI/DTI to study<br>the impact of Alzheimer’s disease pathologies on structural and<br>functional networks among cognitively normal older adults and patients<br>with cognitive impairment. [...]
2024-03-12T16:13:36-04:00Topper, Mackenziehttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;6d6e21b7.2403Re: Discrepancies between timepoints in featquery outputs.
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;48e2449b.2403
Dear Matthew,<br>This is the contents of design.trg:<br>-5.000000e-01 6.752721e+01 1.355544e+02 2.035816e+02 2.716088e+02 106.122440<br>-5.000000e-01 6.752721e+01 1.355544e+02 2.035816e+02 2.716088e+02 106.122440<br><br>It is a block-design, visual stimulus (on & off) design. I attach the ev1 (on) design timing here:<br>0 42 1<br>50 42 1<br>100 42 1<br>150 42 1<br>200 42 1<br><br>thank you!<br><br>Best wishes,<br>Alex
2024-03-12T17:39:22+00:00Sheng Yanghttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;48e2449b.2403Re: Discrepancies between timepoints in featquery outputs.
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;c2f62ef6.2403
Hi Alex,<br>I’ve replied in the other thread.<br><br>Kind Regards<br>Matthew
2024-03-12T17:06:06+00:00Matthew Websterhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;c2f62ef6.2403Re: Discrepancies between timepoints in featquery outputs.
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;979e2eeb.2403
Hi Alex,<br>Can you let me know the contents of “design.trg” in the input feat directory and roughly what sort of design is being used ( especially ev1 )?<br><br>Kind Regards<br>Matthew
2024-03-12T17:05:51+00:00Matthew Websterhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;979e2eeb.2403VBM group template resolution
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;a1d22aac.2403
Hi there,<br><br>It looks like FSLVBM only outputs a gray matter mask with a 2mm isotropic<br>resolution. Is there a way to circumnavigate this to produce a<br>study-specific template with 1mm isotropic voxels?<br><br>Thanks,<br>Christi
2024-03-12T10:37:46+13:00Christi Essexhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;a1d22aac.2403Re: installation set up error
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;579353a5.2403
Hi Sean,<br>The line:<br>export PATH=/opt/homebrew/bin:/Users/seantanyongwei/opt/anaconda3/bin:/Users/seantanyongwei/opt/anaconda3/condabin:/Library/Frameworks/Python.framework/Versions/3.9/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin<br><br>Is probably the one overriding the other settings. If you want to preserve these paths, then adding ${FSLDIR}/share/fsl/bin to the line ( remember all paths are colon separated ) should fix things.<br><br>Kind regards<br>Matthew
2024-03-12T10:20:31+00:00Matthew Websterhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;579353a5.2403Re: FIX installation failing
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;426d2462.2403
Hi Marie,<br>The older instructions are here ( that need to have modified paths ):<br><br>https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind2005&L=FSL&P=R27323<br><br>although it looks like you will need to run this command first to update the conda solver:<br><br>$FSLDIR/bin/conda update -p $FSLDIR conda libmamba -y --solver=classic<br><br>( add sudo if necessary )<br><br>For the 6.0.5 install I think it would be helpful to know the exact error message, but you may also want to try installing the latest FSL ( 6.0.7.8 ) as that includes “pyfix” which is a python-based rewrite of FIX. [...]
2024-03-12T10:12:00+00:00Matthew Websterhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;426d2462.2403Re: fdt_paths and fdt_network_matrix --network mode
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;d0db1f41.2403
Hi Javier<br><br>As far as I recall, the fdt_paths file contains all the streamlines seeded from your seed masks, regardless of whether they have reached the other seed masks you are using in network mode. However, the output matrix (fdt_network_matrix) of course only records the streamlines that connect pairs of ROIs. If you want to check the fdt_paths, you can run ptx separately for each seed mask and set the others as waypoint masks. [...]
2024-03-12T09:01:43+00:00Saad Jbabdihttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;d0db1f41.2403Re: FIX installation failing
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;6689754d.2403
Hello Matthew,<br><br>Thanks for your response.<br><br>I am a bit confused by the commands you mentioned. I could not find them in the instructions. Nevertheless, I tried them and received this message:<br><br>Error while loading conda entry point: conda-libmamba-solver (dlopen(/usr/local/fsl/lib/python3.11/site-packages/libmambapy/bindings.cpython-311-darwin.so, 0x0002): Library not loaded: @rpath/libarchive.19.dylib<br><br>Referenced from: <494304CB-2F24-3FF8-B4AE-F4E6B16BDC26> /usr/local/fsl/lib/libmamba.2.0.0.dylib<br><br>Reason: tried: '/usr/local/fsl/lib/libarchive.19.dylib' (no such file), '/usr/local/fsl/lib/python3.11/site-packages/libmambapy/../../../libarchive.19.dylib' (no such file), '/usr/local/fsl/lib/python3.11/site-packages/libmambapy/../../../libarchive.19.dylib' (no such file), '/usr/local/fsl/bin/../lib/libarchive.19.dylib' (no such file), '/usr/local/fsl/bin/../lib/libarchive.19.dylib' (no such file), '/usr/local/lib/libarchive.19.dylib' (no such file), '/usr/lib/libarchive.19.dylib' (no such file, not in dyld cache)) [...]
2024-03-12T02:21:42+00:00Marie-Eve Hoepplihttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;6689754d.2403Re: randomise with several voxel-dependent EVs
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;2b2a610d.2403
Dear Matthew et al,<br><br>Now that I am looking at the design matrix... It will have more columns than rows. Unless randomise collapses them in some way when dealing with validity masks, I do not see how even a single validity mask per subject can be incorporated into the design. What does randomise do with them? [...]
2024-03-11T23:34:28+00:00Roman Fleysherhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;2b2a610d.2403Re: installation set up error
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;9c5ebb8.2403
Hi Paul,<br><br>Thanks verymuch, yes it seems to be a conda initialisation process (as below). How should I modify this profile?<br><br>Thanks,<br>Sean<br><br>(base) seantanyongwei@seans-Air ~ % cat ~/.zshrc<br><br># >>> conda initialize >>><br><br># !! Contents within this block are managed by 'conda init' !!<br><br>__conda_setup="$('/Users/seantanyongwei/opt/anaconda3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)"<br><br>if [ $? -eq 0 ]; then [...]
2024-03-11T23:15:19+00:00TAN, Sean (ROYAL PAPWORTH HOSPITAL NHS FOUNDATION TRUST)https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;9c5ebb8.2403UK HE survey of carers
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;e16a2473.2403
Apologies for cross-posting<br><br>Dear Colleagues<br>I am sharing this final call as we will be closing our survey of carers in UK HE at the end of the month. Many thanks to those of you who have replied.<br><br>To be eligible, you need to be employed by a UK-based university and to be a carer (broadly understood, including as a parent, for a friend, a relative etc.). Here’s the link:<br>https://angliaruskin.onlinesurveys.ac.uk/national-carers-survey-uk The outcomes will help us to better understand the experiences of carers in higher education and to provide recommendations to the sector.<br>We have received ethical approval for this [...]
2024-03-11T17:59:51+00:00Marie Moreauhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;e16a2473.2403Re: Using fslcc to correlate Melodic_IC to BrainMap RSN template
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;5b061a19.2403
Hi Xiyue,<br><br>The results of fslcc will be meaningless if your images are not aligned with each other. You will need to calculate a registration between talairach and MNI space, and then transform your melodic results into MNI, before you can compare them with the rsn20 images.<br><br>Paul
2024-03-11T16:59:14+00:00Paul McCarthyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;5b061a19.2403Re: Feat command not found
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;a4e26c3.2403
Hi Eddie,<br><br>There should not be any soft/symbolic links in either $FSLDR/bin/ or $FSLDIR/share/fsl/bin/. $FSLDIR/bin/ should contain the actual FSL executables (along with a range of other executable files), and $FSLDIR/share/fsl/bin/ should contain "wrapper" scripts for each of them - this is further described at https://fsl.fmrib.ox.ac.uk/fsl/docs/#/install/configuration?id=fsl-executable-directory-fsldirbin-and-fsldirsharefslbin<br><br>Can you check that the FSL configuration steps are being applied, by running "echo $FSLDIR" and "echo $PATH"? Do you have any other shell configuration files, such as ~/.profile or ~/.bashrc, which might be overriding your environment variables?
2024-03-11T16:52:04+00:00Paul McCarthyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;a4e26c3.2403Re: Eddy Problem : DIfferent matrix size between AP/PA b0 images and main dwi image
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;692a5542.2403
Hi Alejandro,<br><br>Your mask needs to have the same dimensions as your data (and be aligned when viewed in FSLeyes). How did you create your mask image?<br><br>Paul
2024-03-11T16:47:16+00:00Paul McCarthyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;692a5542.2403Re: fsleyes: incorrect gray level
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;947fd629.2403
Hi Roman,<br><br>The setting is just called "Interpolation" - change it to "No interpolation".<br><br>By default, interpolation is turned on when you open a 3D view. If you don't want this to happen, you can start FSLeyes with the --no3DInterp option (or add it as a default command-line argument as outlined at https://open.win.ox.ac.uk/pages/fsl/fsleyes/fsleyes/userdoc/command_line.html#default-command-line-arguments) [...]
2024-03-11T16:42:56+00:00Paul McCarthyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;947fd629.2403Re: installation set up error
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;d10c1835.2403
Hi Sean,<br><br>You probably have another profile file which is overwriting the $PATH - do you have a ~/.zshrc file? What is its contents?<br><br>Paul
2024-03-11T16:40:09+00:00Paul McCarthyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;d10c1835.2403Discrepancies between timepoints in featquery outputs.
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;2dfd0c3e.2403
(the previous post did not show the contents so I'm reposting.)<br><br>Dear FSL experts,<br>I am using featquery to examine %BOLD signal change and to extract peristimulus data. My input to featquery (tfMRI.feat) has 332 timepoints.<br><br>When examining featquery outputs, I found that mean_mask_ts.txt and tsplotc_zstat1.txt (data averaged over all voxels in all sig. clusters for contrast 1) both have 332 timepoints, but ps_tsplotc_zstat1_ev1.txt (model fits averaged over multiple stimulus repeats) has 483 rows. I am not sure why there’s discrepancies in timepoints. [...]
2024-03-11T12:50:37+00:00Alex Yanghttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;2dfd0c3e.2403[reminder] Birmingham-Leiden Summer School in Computational Social Cognition 2024
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;679ee9f9.2403
(Apologies for cross-posting)<br><br>FINAL REMINDER:<br><br>We are delighted to welcome applications for the first edition of the<br>Birmingham-Leiden<br>summer school in Computational Social Cognition (CSC).<br><https://www.compsoccog.com/> The summer school is hosted at the University<br>of Birmingham (UK), in collaboration with Leiden University (NL), and will<br>take place from 15th-17th July 2024. Apply by *14th March 2024* (see<br>information below)! [...]
2024-03-11T12:29:52+00:00Lei Zhanghttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;679ee9f9.2403Discrepancies between timepoints in featquery outputs.
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;e77276.2403
10623.79185<br>10589.34135<br>10562.7296<br>10545.20888<br>10536.7884<br>10542.01292<br>10532.40746<br>10529.08594<br>10514.0319<br>10519.73058<br>10520.68128<br>10524.06868<br>10520.58067<br>10518.78087<br>10513.11874<br>10490.74251<br>10478.33595<br>10476.58887<br>10469.84193<br>10442.59592<br>10427.63754<br>10438.57498<br>10459.73859<br>10459.54719<br>10459.76765<br>10459.52224<br>10473.27613<br>10476.31944<br>10471.04281<br>10462.04316<br>10459.37938<br>10464.38159<br>10460.06558<br>10462.22881<br>10445.64594<br>10446.3604<br>10455.08769<br>10453.76104<br>10470.7869<br>10481.96664<br>10499.60311<br>10532.24483<br>10523.33937<br>10522.41515<br>10511.17011<br>10526.48825<br>10526.80326<br>10524.81208<br>10513.64841<br>10511.33603<br>10555.56529<br>10552.12194<br>10555.4032<br>10568.01522<br>10567.86869<br>10566.3626<br>10529.34156<br>10528.72429<br>10493.20466<br>10464.00521<br>10444.01305<br>10448.75253<br>10418.33207<br>10400.31737<br>10386.22224<br>10390.18087<br>10402.02826<br>10413.40287<br>10432.75703<br>10440.68523<br>10449.80252<br>10445.15768<br>10459.04521<br>10469.10486<br>10479.01267<br>10481.57013<br>10492.39086<br>10520.94462<br>10543.2789<br>10557.83105<br>10568.67472<br>10572.06971<br>10572.81043<br>10550.537<br>10521.66725<br>10513.36229<br>10521.22258<br>10507.1134<br>10487.38682<br>10498.75703<br>10520.08242<br>10509.013<br>10508.02333<br>10497.50316<br>10489.53998<br>10484.07318<br>10473.18392<br>10457.50256<br>10467.76678<br>10464.09066<br> [...]
2024-03-11T10:24:17+00:00Alex Yanghttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;e77276.2403Re: Using fslcc to correlate Melodic_IC to BrainMap RSN template
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;d8877118.2403
Hi,<br><br>FYI, I used 3dresample to convert the template file into the same size as my ICA results. Then I run fslcc and it works.<br><br>3dresample -master melodic_IC.nii.gz -prefix rsn20_resample -input rsn20.nii.gz<br><br>Thank you for your attention.<br><br>Best,<br>Xiyue Zhang<br>PhD candidate in Neuroscience/Doctorante en Neuroscience<br>Speech and hearing Neuroscience Laboratory/Laboratoire des neurosciences de la parole et de l’audition<br>Université Laval<br>Email/Courrier: xiyue.zhang.2@ulaval.ca<br>Hear my name<https://namedrop.io/xiyuezhang> [...]
2024-03-11T03:27:00+00:00Xiyue Zhanghttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;d8877118.2403VBM step C template missing?
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;11086c93.2403
Using fslvbm—on step “C” create the template—segments and makes files that appear to use the template.<br><br>ie<br>_struc_GM_to_T_init_warp.msf<br>_struct_GM_to_T.mat<br>_struc_GM_to_T.nii.gz<br><br>But—there is no “template_GM_4D” image—and no error message.<br><br>Help?<br><br>-- Dan<br><br>The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> .<br>Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender [...]
2024-03-09T13:08:32+00:00Dickstein, Daniel Phttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;11086c93.2403Feat command not found
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;9acfe8a0.2403
Hello,<br><br>I recently installed FSL 6.0.7.7 on Rocky Linux 8. My .bash_profile is set as:<br><br># FSL Setup<br>FSLDIR=/usr/local/software/fsl<br>PATH=${FSLDIR}/share/fsl/bin:${PATH}<br>export FSLDIR PATH<br>. ${FSLDIR}/etc/fslconf/fsl.sh<br><br>When I attempt to run the "Feat" command, it says the command is not found. I noticed that the soft links for Feat and others are only located in $FSLDIR/bin. Why are these soft links not also located in $FSLDIR/share/fsl/bin? Should I also add $FSLDIR/bin to the PATH in order to use these soft links? [...]
2024-03-08T20:06:19+00:00Edward Zunigahttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;9acfe8a0.2403Using fslcc to correlate Melodic_IC to BrainMap RSN template
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;fb661eef.2403
Hi experts,<br><br>I have got the results of ICA from Melodic. The size of melodic_IC is:<br><br>dim1 54<br><br>dim2 64<br><br>dim3 50<br><br>dim4 20<br><br>pixdim1 3.000000<br><br>pixdim2 3.000000<br><br>pixdim3 3.000000<br><br>pixdim4 2.398998<br><br>Data Axes Orientation:<br><br>first (x) = Right-to-Left<br><br>second (y) = Anterior-to-Posterior<br><br>third (z) = Inferior-to-Superior<br><br>Since I used Talairach templates for registration in preprocessing, the melodic_IC’s Template Space is TLRC. The rsn20.nii.gz (download from https://www.fmrib.ox.ac.uk/datasets/brainmap+rsns/) is in MNI space. Do I have to convert my results to MNI? Or convert rsn20.nii.gz to TLRC? [...]
2024-03-08T20:01:19+00:00Xiyue Zhanghttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;fb661eef.2403Re: fsleyes: incorrect gray level
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;547db758.2403
Dear Paul,<br><br>I noticed the issue happens after I exit 3D view. I searched in "settings" and found "interpolate colour maps". I am not sure this is the setting you meant. It is unchecked.<br><br>Roman
2024-03-08T20:00:09+00:00Roman Fleysherhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;547db758.2403Re: fsleyes: incorrect gray level
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;620958ee.2403
How do I turn interpllation off?<br><br>Roman
2024-03-08T19:53:41+00:00Roman Fleysherhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;620958ee.2403Re: installation set up error
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;a202429b.2403
Hi Paul,<br><br>I have updated my z.profile but it still does not seem to be working, below is my list of contents in my z.profile and what happens when i do echo $PATH in my terminal. Is there any indication of what I need to modify?<br><br>Sean<br><br>(base) seantanyongwei@seans-Air ~ % cat ~/.zprofile [...]
2024-03-08T17:21:20+00:00TAN, Sean (ROYAL PAPWORTH HOSPITAL NHS FOUNDATION TRUST)https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;a202429b.2403Re: MMORF complaining error
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;12705eb1.2403
Hi James,<br><br>Are you using a Linux system? At the moment, MMORF can only be used on Linux, and cannot be used on macOS, as Apple do not support CUDA.<br><br>Paul
2024-03-08T09:50:29+00:00Paul McCarthyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;12705eb1.2403MMORF complaining error
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;b2e1ecdf.2403
Hi - I am trying to compile and run MMORF. I have FSL 6.0.7.4 installed.<br><br>When trying to set it up, I get this error:<br><br>$FSLDIR/bin/conda create -c conda-forge -p ~/gcc8 "gxx_linux-64=8.*" make<br><br>Collecting package metadata (current_repodata.json): done<br>Solving environment: unsuccessful attempt using repodata from current_repodata.json, retrying with next repodata source.<br>Collecting package metadata (repodata.json): done<br>Solving environment: failed [...]
2024-03-08T09:33:02+00:00James Garrardhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;b2e1ecdf.2403Re: installation set up error
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;fb1c227e.2403
Hi Sean,<br><br>It looks like the installer wasn't able to update your shell profile. Can you open ~/.zprofile in a text editor, and replace whatever FSL configuration is already in there (if any) with the following:<br><br># FSL Setup<br>FSLDIR=/usr/local/fsl<br>PATH=${FSLDIR}/share/fsl/bin:${PATH}<br>export FSLDIR PATH<br>. ${FSLDIR}/etc/fslconf/fsl.sh<br><br>And then close+reopen your terminal window. If FSL still isn't working, then it means that there may be some other commands in your shell profile which are interfering with the FSL configuration (e.g. overwriting your $PATH variable). [...]
2024-03-08T09:21:15+00:00Paul McCarthyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;fb1c227e.2403FSLVBM Query
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;7d606aeb.2403
Good morning,<br><br>I am a neuroscience PhD student at Auckland University of Technology, New<br>Zealand. I work primarily with MRI and as such use the FSL/FMRIB toolbox<br>regularly, however, I have run into an issue attempting to build a<br>study-specific template. I was hoping to get some assistance with the below:<br><br>I would like to build a study-specific T1w template, rather than<br>registering my images to a standard space (MNI152 or similar). I have run<br>these images through the FSLVBM pipeline which produces a fantastic<br>template. However, this is unfortunately at 2mm isotropic resolution<br>(likely registering images to the MNI152 [...]
2024-03-08T07:11:08+13:00Christi Essexhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;7d606aeb.2403Eddy Problem : DIfferent matrix size between AP/PA b0 images and main dwi image
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;16863616.2403
Dear fsl experts, I hope you may be able to help me with this problem I am facing with eddy<br><br>When I try to run eddy I get the following error:<br>EddyInputError: --imain and --mask images must have the same dimensions<br>Terminating program<br><br>Inspecting the mask and the main image I get the following:<br>fslinfo topup/*_mask.nii.gz<br>data_type INT16<br>dim1 100<br>dim2 100<br>dim3 60<br>dim4 1<br>datatype 4<br>pixdim1 2.200000<br>pixdim2 2.200000<br>pixdim3 2.200000<br>pixdim4 1.000000<br>cal_max 1.000000<br>cal_min 0.000000<br>file_type NIFTI-1+ [...]
2024-03-08T01:53:41+00:00Alejandro Garmahttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;16863616.2403Re: xtract_qc error
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;5b402f2.2403
Hi,<br><br>Unfortunately, there isn't currently a way to perform such an update. However, a new version of FSL should be available in the coming days/by mid next week.<br><br>Thanks,<br>Shaun.
2024-03-07T19:35:54+00:00Shaun Warringtonhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;5b402f2.2403Re: xtract_qc error
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;412ae51e.2403
Thanks for the update Shaun. I talked to our HPC cluster admin and apparently they cannot do a an in-place update of FSL subprograms, they can only re-install the whole FSL package. They did this yesterday, but xtract_qc is still presenting the same error so I assume that the re-install did not include the updated xtract_qc. Is there another way to get the xtract_qc updated as part of the installation process of FSL 6.0.7.8? [...]
2024-03-07T14:41:57+00:00Estephan J. Moana-Filhohttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;412ae51e.2403Re: installation set up error
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;90102e26.2403
Hi Paul,<br><br>After using a different network I have downloaded FSL succes on my Mac. However when I am attempting to run checks to assess if FSL is running correctly, it seems to not be doing so (i logged out then logged back into my terminal). Attached below is the FSL directory in my system at the moment, and my attempts to run some commands which failed. Could you please advise on this? Many thanks, Sean [...]
2024-03-07T11:29:33+00:00TAN, Sean (ROYAL PAPWORTH HOSPITAL NHS FOUNDATION TRUST)https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;90102e26.2403Re: oxford_asl_roi_stats
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;33f86e7d.2403
Yes, oxford_asl adds these ROIs into the region analysis script using the following options:<br><br>--roi-native gmmask_pure_cort.nii.gz wmmask_pure_cereb.nii.gz<br><br>You can do the same in your manual run, however one slight problem is that these ROIs are saved in the output under different names to the ones used internally in oxford_asl. They are saved as native_space/cortical_gm_roi and native_space/cerebral_wm_roi. If you pass these to the ROI analysis script using --roi-native then you will get the same numbers but the naming (which is derived from the filename) will be different. [...]
2024-03-07T10:49:07+00:00Martin Craighttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;33f86e7d.2403Re: fsleyes: incorrect gray level
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;612068dc.2403
Hi Roman,<br><br>I can't quite tell from the screenshot, but it looks like you have interpolation enabled, which will cause smoothing across voxels.<br><br>Paul
2024-03-07T09:13:55+00:00Paul McCarthyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;612068dc.2403(Forgot attachments) b0 intensities higher than b1000
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;a1604d97.2403
Dear FSL experts,<br><br>I have come across a problem that I am having some difficulty resolving<br>in the DWI dataset I am working with. I would like to have your opinion on<br>it.<br><br>Providing a brief overview:<br><br>1. My sequence consists of:<br>- 1 acquisition of b0 AP (7 volumes)<br>- 1 acquisition of b0 PA (2 volumes)<br>- 1 acquisition of 1 b0 AP, 32 b1000, and 32 b2000 (65 volumes)<br>In my case, I am only using the b0 that was acquired with the other b<br>values for reasons related to the scanner (the separately acquired b0s had<br> [...]
2024-03-07T08:57:11+00:00Nelson Descalçohttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;a1604d97.2403b0 intensities higher than b1000
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;485b8239.2403
Dear FSL experts,<br><br>I have come across a problem that I am having some difficulty resolving<br>in the DWI dataset I am working with. I would like to have your opinion on<br>it.<br><br>Providing a brief overview:<br><br>1. My sequence consists of:<br>- 1 acquisition of b0 AP (7 volumes)<br>- 1 acquisition of b0 PA (2 volumes)<br>- 1 acquisition of 1 b0 AP, 32 b1000, and 32 b2000 (65 volumes)<br>In my case, I am only using the b0 that was acquired with the other b<br>values for reasons related to the scanner (the separately acquired b0s had<br> [...]
2024-03-07T08:49:31+00:00Nelson Descalçohttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;485b8239.2403tbss_skeleton
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;844bae8b.2403
Full message available at: <a href="https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;844bae8b.2403">tbss_skeleton</a>2024-03-06T22:48:35+00:00Lisette LeMerisehttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;844bae8b.2403tbss_skeleton for nonFA: adapt normal tbss or use -a flag?
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;56085ce7.2403
Hi all!<br><br>I hope you are well, and thank you for FSL and a place to ask questions!<br><br>I have some quick questions regarding the different ways to go about non-FA TBSS.<br><br>First, I know that, with tbss_non_fa, it adapts the tbss_skeleton command for its final component to also have the -a flag for alternative 4D data. That said, when I ran this command for my various parameters: [...]
2024-03-06T22:41:31+00:00Lisette LeMerisehttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;56085ce7.2403Re: randomise with several voxel-dependent EVs
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;7fa413f0.2403
Dear Matthew,<br><br>Images with validity masks are all 0s and 1s: 1 in pixels where data is valid, 0 is where data is invalid. Yes, they are subject specific and EV specific.<br><br>Perhaps to give artificial example, I have a model:<br><br>FA = age + sex + CBF + fMRI<br><br>Each subject has 3 images that come from 3 acquisitions with different FOVs. Thus, there are voxels where all 3 are valid. There are voxels where FA and CBF are valid, but fMRI is not and so on. These combinations vary from subject to subject. That is, there are voxels [...]
2024-03-06T18:02:07+00:00Roman Fleysherhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;7fa413f0.2403fsleyes: incorrect gray level
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;cff6e62f.2403
Dear Paul,<br>Dear FSL developers,<br><br>I noticed that fsleyes sometimes does not show gray (perhaps color in general) correctly.<br>Loaded is a NIFTI file with two time points in it. Volume=0 is T1W image, volume=1 is a mask of only 0s and 1s. As you can see on the image, pixel brightness at crosshairs is gray despite value reads 1 and should be white (max of brightness range). [...]
2024-03-06T17:52:34+00:00Roman Fleysherhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;cff6e62f.2403Re: randomise with several voxel-dependent EVs
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;b9b9be5d.2403
Dear Roman,<br>Can you confirm how the validity masks are coded ( e.g. what does 0 and 1 mean ), if they are subject specific, and if the validity is in/exclusive ( e.g. can a brain voxel have any combination of EV1/EV2 validity )?<br><br>Kind Regards<br>Matthew
2024-03-06T17:05:05+00:00Matthew Websterhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;b9b9be5d.2403Re: oxford_asl_roi_stats
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;68b299d1.2403
Hi Martin,<br><br>you are right. I tried both approaches with another project and yielded the same results. There might be an error in my other script (I use GNU parallel to run many subjects in parallel, maybe there is something wrong in scripting). However, I noticed that the csv files in the oxford_asl approach contain gmmask_pure_cort and wmmask_pure_cereb, which is not present in the oxford_asl_roi_stats approach. This might be problematic when someone extracts values from the csv file in certain rows using both approaches. [...]
2024-03-06T16:09:04+00:00Ralf Veithttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;68b299d1.2403Re: Eddy Fieldmap Wrapping
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;5de2f914.2403
Hi Jesper,<br><br>Thanks again for looking into this. Have you been able to recreate the issue I was having?<br><br>Best,<br>Bram<br><br>From: Bram Diamond <bramdiamond@gmail.com><br>Date: Friday, March 1, 2024 at 2:27 PM<br>To: FSL - FMRIB's Software Library <FSL@JISCMAIL.AC.UK><br>Subject: Re: [FSL] Eddy Fieldmap Wrapping<br>Here is the eddy command:<br><br>eddy_cpu --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --field= fmap_hz2dwi_12dof_applyxfm --slm=linear --data_is_shelled --out=dwi_post_eddy --verbose [...]
2024-03-06T15:19:09+00:00Bram Diamondhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;5de2f914.2403Re: oxford_asl_roi_stats
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;29e959e0.2403
Hi Ralf,<br><br>I just tried this and got the same results by running the script manually. The command line I used was:<br><br>oxford_asl_roi_stats --oxasl-output oxford_asl_output/native_space/ --fslanat T1.anat --output roi_stats_test --add-standard-atlases<br><br>Is this the same as what you're doing? And did your oxford_asl run use the same fslanat output?<br><br>Only other thing I can think is whether you could be comparing PV corrected results in native_space/pvcorr with non-PVC results in native_space? [...]
2024-03-06T14:40:09+00:00Martin Craighttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;29e959e0.2403Re: HRF estimation
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;e6096af2.2403
try it!<br>https://www.fmrib.ox.ac.uk/datasets/techrep/tr04mw2/tr04mw2.pdf<br><br>Am 06.03.24, 12:53 schrieb "FSL - FMRIB's Software Library im Auftrag von Sheng Yang" <FSL@JISCMAIL.AC.UK im Auftrag von 0000c313628a5f61-dmarc-request@JISCMAIL.AC.UK>:<br><br>Dear Andreas,<br>I have total of 5 blocks in 1 run, which consisted of 20s of stimulus then 8s of crosshair (off).<br><br>Thank you,<br>Alex
2024-03-06T13:38:18+01:00Andreas Bartschhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;e6096af2.2403Re: Diffusion preprocessing questions
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;94adf318.2403
Dear Victoria,<br><br>Thank you for the advice and explanation! I have one follow-up question regarding your explanation for why the rotations would differ when the first shell was preprocessed alone compared to when it was preprocessed combined with the second shell. In both cases the b=0 volume used for eddy was the first b=0 volume from the first shell so would this mean the bvec values should be the same for the first shell in both scenarios because it is relative to the same b=0 volume, or is there something about the inclusion of the volumes from the second shell [...]
2024-03-06T11:57:41+00:00Jesper Anderssonhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;94adf318.2403Re: HRF estimation
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;dfc8d2ca.2403
Dear Andreas,<br>I have total of 5 blocks in 1 run, which consisted of 20s of stimulus then 8s of crosshair (off).<br><br>Thank you,<br>Alex
2024-03-06T11:52:54+00:00Sheng Yanghttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;dfc8d2ca.2403Re: HRF estimation
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;16be1fd.2403
Hi Alex,<br><br>you could try FLOBS.<br>How long are your blocks?<br><br>Cheers,<br>Andreas<br><br>Am 06.03.24, 12:34 schrieb "FSL - FMRIB's Software Library im Auftrag von Alex Yang" <FSL@JISCMAIL.AC.UK im Auftrag von 0000c313628a5f61-dmarc-request@JISCMAIL.AC.UK>:<br><br>Hello FSL experts,<br>I am analysing a block-design, visual stimulus data (on and off).<br><br>In FSL, I have d pre-processing of data. Then, using feat, activation modelling (first-level analysis of each subject) was performed using Feat. For convolution setting I set as canonical HRF (double-gamma). [...]
2024-03-06T12:45:20+01:00Andreas Bartschhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;16be1fd.2403HRF estimation
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;61acd928.2403
Hello FSL experts,<br>I am analysing a block-design, visual stimulus data (on and off).<br><br>In FSL, I have d pre-processing of data. Then, using feat, activation modelling (first-level analysis of each subject) was performed using Feat. For convolution setting I set as canonical HRF (double-gamma).<br><br>I want to derive subject-level HRF characteristics within the anatomical region of V1, to be more specific, magnitude of change (%), time-to-peak, time-to-baseline. I know that activation effect size (or magnitude of change) can be derived using Featquery within FSL. [...]
2024-03-06T11:33:57+00:00Alex Yanghttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;61acd928.2403Re: Diffusion preprocessing questions
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;ad7e1af5.2403
Hi Jesper,<br><br>Thank you for the advice and explanation! I have one follow-up question regarding your explanation for why the rotations would differ when the first shell was preprocessed alone compared to when it was preprocessed combined with the second shell. In both cases the b=0 volume used for eddy was the first b=0 volume from the first shell so would this mean the bvec values should be the same for the first shell in both scenarios because it is relative to the same b=0 volume, or is there something about the inclusion of the volumes from the second shell [...]
2024-03-06T03:41:43+00:00Victoria Rosenhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;ad7e1af5.2403Re: DOF cannot be zero or negative!
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;6187715.2403
Hi Roberto,<br>The masks are not specifically anatomical but removing voxels with ( essentially ) no variance. For one of the problematic subjects you can re-run the commands<br><br>fslmaths <subjectData> -Tstd mask1<br>fslmaths <subjectData> -Tstd -bin mask2<br><br>To check both the temporal standard-deviation of that image ( mask1 ) and the binarised version that dual_regression would use ( mask2 ). You can also check the time-series view of brain voxels for the same subject with FSLeyes to see what the in-brain signals look like. [...]
2024-03-05T20:07:25+00:00Matthew Websterhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;6187715.2403Re: DOF cannot be zero or negative!
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;5acca9c0.2403
Hi Matthew<br><br>Thanks for your assistance. I have some follow up questions. Firstly,<br>I don't entirely understand the output of dual regression. Are the volumes<br>of maskALL supposed to represent anatomical masks of each subject? The<br>subjects with problematic data are blank (such as volume 57 that you<br>showed), but the others don't look like brains (such as volume 56 below).<br>Also, the "dr_stage1_subject.txt" file for all subjects is just filled with<br>0s. [...]
2024-03-05T15:48:32+00:00Roberto Dos Santoshttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;5acca9c0.24032 PhD positions in layer-fMRI of high-level cognition at the Max Planck Institute for Biological Cybernetics in Tübingen, Germany
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;bc5807a3.2403
The newly established Cognitive Neuroscience & Neurotechnology group led by Dr. Romy Lorenz is looking for two enthusiastic PhD students (m/f/d) to join our growing team at the Max Planck Institute for Biological Cybernetics in Tübingen, Germany.<br><br>Our lab focuses on advancing our understanding of the frontoparietal brain network mechanisms that underpin high-level cognition and adaptive behaviour. For this, we pursue an interdisciplinary research programme that allows studying this brain system at multiple levels of granularity. Our methodology involves subject-specific brain-computer interface technology, fMRI at 3T and ultrahigh (i.e., 7T and 9.4T) magnetic field strengths (for resolving cortical layers), EEG, [...]
2024-03-05T15:06:25+01:00Romy Lorenzhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;bc5807a3.2403Re: installation set up error
https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;968eaf4d.2403
Hi Sean,<br><br>It looks like some network connections are being blocked - I'm guessing you are connecting to the internet though an institutional network (e.g. a hospital)? Do you have a local IT administrator who might be able to help?<br><br>An alternative option would be to try installing FSL whilst connected to a different network (e.g. home, university, etc). [...]
2024-03-05T10:17:54+00:00Paul McCarthyhttps://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;968eaf4d.2403