Hi SPM Expert
I am new on SPM . I wouldlike to know that where should i get suitable data of fmri. ? .it will be great that if any body share dataset. ?

Thanks

Best Regards
Toufique

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From: SPM automatic digest system
Sent: Tuesday, 7 June, 9:06 a.m.
Subject: SPM Digest - 5 Jun 2016 to 6 Jun 2016 (#2016-162)
To: SPM (Statistical Parametric Mapping)

There are 16 messages totaling 9254 lines in this issue. Topics of the day: 1. ROI analysis in fMRI 2. R: [SPM] Deformation estimation from different modalities ? 3. Covariate analysis 4. amyloid PET template (2) 5. model estimation error 6. SPM12 origin reset 7. MFX contrasts 8. Regarding Coorelation between the estimated and true effects. 9. FW: [SPM] Changing fields in SPM.mat (2) 10. Introduction to Neuroimaging text (2) 11. substracting 2 con images for one subject 12. Second Call for Papers 13. CAT12 Contrasts - 2x2 ANOVA Longitudinal Study ---------------------------------------------------------------------- Date: Mon, 6 Jun 2016 06:55:16 +0100 From: Shilpi Modi Subject: ROI analysis in fMRI Hi SPMers, After carrying out single subject analysis of my fMRI data, I extracted BOLD contrast estimates from a priori ROIs using MarsBaR toolbox. The contrast estimates showed positive correlation with behavioral data. However, on performing whole brain multiple regression analysis (using SPM) between con images of all the subjects and behavioural data on the ROI masks, no correlation was obtained. Can someone please explain, why it can be so?? Regards, Shilpi Modi, Scientist, NMR Research Centre, INMAS, Lucknow Road, Timarpur, Delhi-54 India ------------------------------ Date: Mon, 6 Jun 2016 07:45:08 +0000 From: PRESOTTO LUCA Subject: Re: R: [SPM] Deformation estimation from different modalities ? Hi Gabriel, Yes, you just need to mean the 60 (MRI-normalized) PET images. Keep in mind, however, that, due to different tracer uptake levels, if you straight up mean all the images you have, you aren't giving them equal statistical weighting, so to say. Therefore it is better to scale each image to some identical reference beforehand (e.g.: global mean). In this scope it's not really relevant which scaling procedure you use. BTW, be careful of (eventual) areas that might be missing in some images. cheers, Luca ________________________________ Da: gabriel robert Inviato: domenica 5 giugno 2016 22.08.27 A: PRESOTTO LUCA Oggetto: Re: [SPM] R: [SPM] Deformation estimation from different modalities ? Hi Luca, Thanks for your reply, I'll go for the second option. In order to generate my PET template from the 60 normalized PET, do I just have to mean the 60 PET's ? Thanks Gabriel 2016-06-04 21:49 GMT+02:00 PRESOTTO LUCA >: Dear Gabriel, I'm not sure about what do you want to do. Specifically, I don't understand what kind of template you want to build (pet or Mr) and what do you want to use it for. In my experience the new normalize doesn't work well for PET. So I'd recommend using just the old normalize routine with a specific PET template for your tracer. Otherwise you could use the new normalize routine on the 60 MRI scans, apply the deformation to the pet, build your own PET template and then use the old normalise. Hope this can help. Cheers, Luca ________________________________ Da: gabriel robert Inviato: ?03/?06/?2016 18:22 A: [log in to unmask] Oggetto: [SPM] Deformation estimation from different modalities ? Hi SPM experts, We have a dataet of 100 PET data but only 60 of them got a proper T1. We'd like to create our own study specific template with our 60 MRI with DARTEL. In order to not introduce bias we'd like to estimate the deformation fields from the PET to the T1 mean image, using DARTEL(existing template), instead of using a standard PET template. However I was wondering if that could be possible given the different image resolution ? Many thanks for your help and time, Gabriel Rispetta l'ambiente: non stampare questa mail se non ? necessario. Respect the environment: if it's not necessary, don't print this mail. IL TUO 5XMILLE AL SAN RAFFAELE DI MILANO Devolvi il tuo 5 per mille all'Ospedale San Raffaele: perch? al centro della Ricerca ci sei TU. CODICE FISCALE: 07636600962, nel riquadro RICERCA SANITARIA. Non c'? cura, senza ricerca. Non c'? ricerca, senza il tuo 5xmille. Scopri come su http://www.5xmille.org [http://www.5xmille.org/img/731x129.jpg] Rispetta l'ambiente: non stampare questa mail se non ? necessario. Respect the environment: if it's not necessary, don't print this mail. IL TUO 5XMILLE AL SAN RAFFAELE DI MILANO Devolvi il tuo 5 per mille all'Ospedale San Raffaele: perch? al centro della Ricerca ci sei TU. CODICE FISCALE: 07636600962, nel riquadro RICERCA SANITARIA. Non c'? cura, senza ricerca. Non c'? ricerca, senza il tuo 5xmille. Scopri come su http://www.5xmille.org [http://www.5xmille.org/img/731x129.jpg] ------------------------------ Date: Mon, 6 Jun 2016 09:18:40 +0100 From: Stijn Michielse Subject: Re: Covariate analysis Dear Helmut, The provided answer exactly what we needed to know. Thanks a lot for helping out! Kind regards, Ing. Stijn Michielse MScRes School for Mental Health and Neuroscience – Division Mental Health Department of Psychiatry & Neuropsychology [log in to unmask] www.maastrichtuniversity.nl ------------------------------ Date: Mon, 6 Jun 2016 09:25:55 +0000 From: PRESOTTO LUCA Subject: Re: amyloid PET template Dear Gayane, You pose an interesting question. Indeed many papers that studied amyloid PET mention the use of an amyloid template, however I haven't found a paper explicitly mentioning how the template was built and its validation. (maybe I didn't look well enough, I didn't spend a lot of time looking... but still even the references are generally not relevant). Anyway, try looking at the ADNI collaboration, they used a template on a number of papers, therefore they should have it somewhere, hopefully available. And I believe that, if an amyloid template can ever work, its validation is fundamental! Amyloid images are characterized by extremely different spatial features between people with no burden and people with a high burden. Those without have a very well defined White matter structure, those with have almost no discernible anatomical features. Therefore I would think that even normalizing "positive" images to a positive template might be problematic, as anatomical features are generally lacking. If you factor into this that positive and negative images are *very* different, I'd say that there is a high chance of such an approach not to work in general and there is a high risk of introducing some serious bias between positive and negative groups. Regards, Luca ________________________________________ Da: SPM (Statistical Parametric Mapping) per conto di Gayane Aghakhanyan Inviato: domenica 5 giugno 2016 09.37.42 A: [log in to unmask] Oggetto: [SPM] amyloid PET template Dear SPM community, I have limited amyloid PET data of two different groups of subjects, unfortunately, without corresponding 3D T1 MRI data. Nonetheless, I'd like to apply voxel-wise between group comparison of amyloid uptake by using an amyloid PET template. Could some suggest me any useful sources where I can find/ask/request an amyloid PET template to be used only for the research proposes? Thank you beforehand, Gayane Aghakhanyan, MD, PhD Resident Physician University of Pisa, Department of Translational Research and of New Surgical and Medical Technology Tel: +393277013870 email: [log in to unmask] Rispetta l’ambiente: non stampare questa mail se non è necessario. Respect the environment: if it's not necessary, don't print this mail. IL TUO 5XMILLE AL SAN RAFFAELE DI MILANO Devolvi il tuo 5 per mille all’Ospedale San Raffaele: perché al centro della Ricerca ci sei TU. CODICE FISCALE: 07636600962, nel riquadro RICERCA SANITARIA. Non c’è cura, senza ricerca. Non c’è ricerca, senza il tuo 5xmille. Scopri come su http://www.5xmille.org [http://www.5xmille.org/img/731x129.jpg] ------------------------------ Date: Mon, 6 Jun 2016 10:31:29 +0100 From: zzang Subject: model estimation error Hi all, I've been consistently running into the error as shown below: " SPM12: spm_est_non_sphericity (v6015) 10:43:10 - 06/06/2016 ======================================================================== Chunk 35/35 : ...done Failed 'Model estimation' Error using spm_est_non_sphericity (line 196) Please check your data: There are no significant voxels. In file "/home/common/matlab/spm12/spm_est_non_sphericity.m" (v6015), function "spm_est_non_sphericity" at line 196. In file "/home/common/matlab/spm12/spm_spm.m" (v6678), function "spm_spm" at line 421. In file "/home/common/matlab/spm12_r6470_20150506/config/spm_run_fmri_est.m" (v5809), function "spm_run_fmri_est" at line 33. No executable modules, but still unresolved dependencies or incomplete module inputs. The following modules did not run: Failed: Model estimation Skipped: Contrast Manager " I've searched for the solution online, including the archives. I checked smoothed data, volume by volume, no missing data; I've changed mask threshold to '-inf', didn't work. I tried a few subjects, thinking it might be something subject specific. not sure, because it worked for some subjects but not all. It really puzzles me. just to clarify, here's what I've done: 1. estimate the confounding effects of WM, CSF and motion, save residuals (p.s. it's the resting state data) 2. extract mean timeseries of ROIs 3. specify ROI mean timeseries as the only regressor in an GLM model with residual scans as the input (separate models for each ROI). Any suggestions/help will be highly appreciated. Best, zzang ------------------------------ Date: Mon, 6 Jun 2016 12:14:57 +0000 From: PRESOTTO LUCA Subject: SPM12 origin reset Dear experts, I'm using SPM12, I've erroneously set some rotations and other things of my images, and I'd like to reset the orientation of the image, as it was common to do in the "display" routine in previous SPM versions. In the manual, it says that there is the same "reset" button in the interfact. However, I can see only the "set origin" and "reorient" buttons. Am I missing something trivial somewhere? (BTW, what is the "set origin" button for? Thank you, Luca Rispetta l’ambiente: non stampare questa mail se non è necessario. Respect the environment: if it's not necessary, don't print this mail. IL TUO 5XMILLE AL SAN RAFFAELE DI MILANO Devolvi il tuo 5 per mille all’Ospedale San Raffaele: perché al centro della Ricerca ci sei TU. CODICE FISCALE: 07636600962, nel riquadro RICERCA SANITARIA. Non c’è cura, senza ricerca. Non c’è ricerca, senza il tuo 5xmille. Scopri come su http://www.5xmille.org [http://www.5xmille.org/img/731x129.jpg] ------------------------------ Date: Mon, 6 Jun 2016 13:09:10 +0000 From: "McMains, Stephanie" Subject: MFX contrasts Hi all, I am trying to make a contrast for a group analysis (level 2) that we used the mixed model, or MFX analysis for. We can't seem to use the contrast manager within the batch system because it keeps giving the error: Contrasts folder : ./MFX/3subj/mfx Failed 'Contrast Manager' Reference to non-existent field 'xBF'. In file "/net/rcss2/srv/export/ncf_tools/share_root/apps/arch/linux_x86_64/spm/12.6225b/config/spm_run_con.m" (v6025), function "spm_run_con" at line 128. The following modules did not run: Failed: Contrast Manager We got the error message when we used the cond/sess way of defining some t-tests. I like to use this method because you only have to think about the conditions you are interested in, not try and figure out how many zeros you have and where they go. Unless someone has a fix for our error above, I will have to do it in on the fly after hitting the results button. Are there any tricks to building this? Are the first three columns our conditions of interest? So if I wanted to contrast our first two conditions I would just need a 1 -1, as it says it zero pads it? Thanks, Stephanie +++++++++++++++++++++++++ Stephanie McMains Neuroimaging Staff Scientist Center for Brain Science Harvard University 52 Oxford Street Cambridge, MA 02138 +++++++++++++++++++++++++ For answers to frequently asked questions: http://cbs.fas.harvard.edu/science/core-facilities/neuroimaging/information-investigators/faq ------------------------------ Date: Mon, 6 Jun 2016 14:59:22 +0000 From: NUML engg Subject: Regarding Coorelation between the estimated and true effects. Dear all, I have a question regarding correlations between the estimated and true effects. I have fMRI data with two classes. How can I do correlation between estimated and true effects with real data? Thanks RegardsNUML    ------------------------------ Date: Mon, 6 Jun 2016 16:03:19 +0000 From: "Afzal, Afsana" Subject: Re: FW: [SPM] Changing fields in SPM.mat Hi, Just following up on the thread below. I've reattached the X.mat file here (not sure if the mailing list will allow it to go through...). Thank you, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ________________________________ From: Afsana Afzal [[log in to unmask]] Sent: Thursday, May 26, 2016 12:45 PM To: Donald McLaren Cc: Afzal, Afsana; [log in to unmask] Subject: Re: FW: [SPM] Changing fields in SPM.mat Hi Donald, The parfile path is being updated properly and does not cause an error. It looks like the error is being caused because there are several absolute paths that are inherited from X.mat. For example, FSFAST2SPM is grabbing the value of config.params.runflac(jj).flac.mri.fspec directly from X.mat's runflac(jj).flac.mri.fspec field (which contains an absolute path to the preprocessed functional data). In this case, because the functional data directory was renamed to 'msit_001' from 'msit', the script errors out because it's using the absolute path stored in X.mat. I've tried to replace all occurrences of the old filepath using spm_changepath but it didn't change all the fields that the FSFAST2SPM uses when filling in the config.params and SPM.mat structures. I've also tried to remove all dependencies on absolute paths but my familiarity with the code is limited and I wasn't able to catch all occurrences so I still kept running into similar errors. I've attached the X.mat file for a given subject here for your inspection. Thank you very much for your time, Afsana On Thu, May 26, 2016 at 12:34 PM, Afzal, Afsana > wrote: ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ________________________________ From: MCLAREN, Donald [[log in to unmask]] Sent: Tuesday, May 24, 2016 11:36 PM To: Afzal, Afsana Cc: [log in to unmask] Subject: Re: [SPM] Changing fields in SPM.mat Afsana, FSFAST2SPM doesn't allow the data and models to be in different locations. The file X.mat doesn't actually contain the path to the data. The current code assumes that the data can be found: [config.Study filesep config.Subject filesep config.Subject_Subdirectory filesep config.params.runflac(1).flac.runlist(1,:) filesep config.params.runflac(1).flac.funcstem '.nii.'] It was setup this way because the X.mat file doesn't contain the directory information or at least I didn't know where the directory information was stored when I wrote the FSFAST2SPM program. I would suggest create a mirror of the FSFAST directory tree in the new location, all that should be needed is (1) the X.mat file; and (2) config.params.runflac(jj).flac.parfile in the new locations. I don't have a current FSFAST analysis setup to test if moving the X.mat and parfiles to the new location will work, but I think it should work as the process doesn't need the results of the FSFAST model, it just needs to know where the inputs. Best, Donald Best Regards, Donald McLaren, PhD On Tue, May 24, 2016 at 10:02 AM, Afzal, Afsana > wrote: Hi Donald, I'm actually trying to change the X.mat file that's created as a result of running the first-level analyses in FSFAST. It seems like spm_changepath is not changing all of the paths in the mat file because I'm getting the following error when running gPPI on the fsfast analysis: Error using spm_vol>subfunc (line 101) File "/autofs/space/lilli_004/users/DARPA-MSIT/hc001/msit/001/fmcpr.sm4.fsaverage.lh.b0dc.nii" does not exist. Error in spm_vol>subfunc1 (line 77) v = subfunc(P(i,:)); Error in spm_vol>subfunc2 (line 69) V = subfunc1(P); Error in spm_vol (line 54) V = subfunc2(P); Error in FSFAST2SPM (line 304) SPM.xY.VY=spm_vol(SPM.xY.P); Error in msit_ppi_wrapper (line 33) FSFAST2SPM(config) I'm not sure which field has remained unchanged and is causing the error. Thanks for you help, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 ________________________________ From: Donald McLaren [[log in to unmask]] Sent: Thursday, May 19, 2016 1:50 PM To: Afzal, Afsana Cc: [log in to unmask] Subject: Re: [SPM] Changing fields in SPM.mat You can do that with spm_changepath. On May 19, 2016, at 10:55 AM, Afzal, Afsana > wrote: Hi everyone, Because of space constraints, I had to move my preprocessed data to a different location. I'm trying to change the filepath information stored in the SPM.mat files to reflect the location change. Is there an easy way to iterate through the matfile and change all the paths (this would save me from having to re-run all of my analyses). Thanks for your help, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078 [log in to unmask] ------------------------------ Date: Mon, 6 Jun 2016 16:30:53 +0000 From: "Gaab, Nadine" Subject: Introduction to Neuroimaging text Hi All, I would like to update readings for a class and I am looking for some recommendations for good readings that cover a (very basic) introduction to neuroimaging techniques (including the basics of MR physics, the BOLD effect, experimental design, diffusion tensor imaging, etc.). Does anyone have a good recommendation? Thank you. Nadine Gaab "If we knew what it was we were doing, it would not be called research, would it?" A. Einstein (1879-1955) Nadine Gaab, PhD Associate Professor of Pediatrics Boston Children's Hospital/Harvard Medical School Department of Medicine/Division of Developmental Medicine Laboratories of Cognitive Neuroscience Mail stop code: BCH3178 1 Autumn Street (Office 643); Boston, MA 02115 [log in to unmask] phone: 857-218-3021 www.gaablab.com ------------------------------ Date: Mon, 6 Jun 2016 13:05:55 -0400 From: Malak abu shakra Subject: substracting 2 con images for one subject Dear SPMers, I was wondering how I could subtract two con images for one subject; I have two conditions: alcohol and placebo, and I would like to obtain the con images for condition one minus condition 2, for each subject at a time. I realize this would be done using 1st level analysis but I'm not quite sure how. Thank you ! -- Malak Abu Shakra Doctoral Candidate Clinical Psychology Psychology Dept. Robert O. Pihl Lab McGill University 1205 Dr. Penfield Avenue Stewart Biology Building - Room W8/37 Montreal, Quebec, H3A 1B1 Canada ------------------------------ Date: Mon, 6 Jun 2016 15:44:33 -0400 From: "MCLAREN, Donald" Subject: Re: FW: [SPM] Changing fields in SPM.mat There are 2 options: (1) Re-run the models through FAST again with the new directories; or (2) Use spm_changepath to fix the errors. For example, change: /autofs/space/lilli_004/users/DARPA-MSIT/hc003/msit/001/ to /autofs/space/lilli_004/users/DARPA-MSIT/hc003/msit_001/001/ Unfortunately, the command changes for each subject (and potentially each run), but its the only way to fix them. Best Regards, Donald McLaren, PhD On Mon, Jun 6, 2016 at 12:03 PM, Afzal, Afsana wrote: > > Hi, > > Just following up on the thread below. I've reattached the X.mat file here > (not sure if the mailing list will allow it to go through...). > > Thank you, > > Afsana > > ______________________________ > *Afsana Afzal* > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > ------------------------------ > *From:* Afsana Afzal [[log in to unmask]] > *Sent:* Thursday, May 26, 2016 12:45 PM > *To:* Donald McLaren > *Cc:* Afzal, Afsana; [log in to unmask] > *Subject:* Re: FW: [SPM] Changing fields in SPM.mat > > Hi Donald, > > The parfile path is being updated properly and does not cause an error. > > It looks like the error is being caused because there are several absolute > paths that are inherited from X.mat. For example, FSFAST2SPM is grabbing > the value of config.params.runflac(jj).flac.mri.fspec directly from > X.mat's runflac(jj).flac.mri.fspec field (which contains an absolute path > to the preprocessed functional data). In this case, because the functional > data directory was renamed to 'msit_001' from 'msit', the script errors out > because it's using the absolute path stored in X.mat. > > I've tried to replace all occurrences of the old filepath using > spm_changepath but it didn't change all the fields that the FSFAST2SPM uses > when filling in the config.params and SPM.mat structures. I've also tried > to remove all dependencies on absolute paths but my familiarity with the > code is limited and I wasn't able to catch all occurrences so I still kept > running into similar errors. > > I've attached the X.mat file for a given subject here for your inspection. > > Thank you very much for your time, > > Afsana > > > On Thu, May 26, 2016 at 12:34 PM, Afzal, Afsana > wrote: > >> >> >> >> ______________________________ >> *Afsana Afzal* >> Clinical Research Coordinator >> Massachusetts General Hospital >> Division of Neurotherapeutics >> Department of Psychiatry: Neurosciences >> 149 13th St, Room 2612 >> Charlestown, MA 02129 >> Phone: 617-643-5129 >> Fax: 617-726-4078 >> ------------------------------ >> *From:* MCLAREN, Donald [[log in to unmask]] >> *Sent:* Tuesday, May 24, 2016 11:36 PM >> *To:* Afzal, Afsana >> *Cc:* [log in to unmask] >> *Subject:* Re: [SPM] Changing fields in SPM.mat >> >> Afsana, >> >> FSFAST2SPM doesn't allow the data and models to be in different >> locations. The file X.mat doesn't actually contain the path to the data. >> >> The current code assumes that the data can be found: >> >> [config.Study filesep config.Subject filesep config.Subject_Subdirectory >> filesep config.params.runflac(1).flac.runlist(1,:) filesep >> config.params.runflac(1).flac.funcstem '.nii.'] >> >> It was setup this way because the X.mat file doesn't contain the >> directory information or at least I didn't know where the directory >> information was stored when I wrote the FSFAST2SPM program. >> >> I would suggest create a mirror of the FSFAST directory tree in the new >> location, all that should be needed is (1) the X.mat file; and (2) >> config.params.runflac(jj).flac.parfile in the new locations. I don't have a >> current FSFAST analysis setup to test if moving the X.mat and parfiles to >> the new location will work, but I think it should work as the process >> doesn't need the results of the FSFAST model, it just needs to know where >> the inputs. >> >> >> Best, >> >> Donald >> >> Best Regards, >> Donald McLaren, PhD >> >> >> On Tue, May 24, 2016 at 10:02 AM, Afzal, Afsana >> wrote: >> >>> Hi Donald, >>> >>> I'm actually trying to change the X.mat file that's created as a result >>> of running the first-level analyses in FSFAST. It seems like spm_changepath >>> is not changing all of the paths in the mat file because I'm getting the >>> following error when running gPPI on the fsfast analysis: >>> >>> Error using spm_vol>subfunc (line 101) >>> File >>> "/autofs/space/lilli_004/users/DARPA-MSIT/hc001/msit/001/fmcpr.sm4.fsaverage.lh.b0dc.nii" >>> does not exist. >>> >>> Error in spm_vol>subfunc1 (line 77) >>> v = subfunc(P(i,:)); >>> >>> Error in spm_vol>subfunc2 (line 69) >>> V = subfunc1(P); >>> >>> Error in spm_vol (line 54) >>> V = subfunc2(P); >>> >>> Error in FSFAST2SPM (line 304) >>> SPM.xY.VY=spm_vol(SPM.xY.P); >>> >>> Error in msit_ppi_wrapper (line 33) >>> FSFAST2SPM(config) >>> >>> I'm not sure which field has remained unchanged and is causing the >>> error. >>> >>> Thanks for you help, >>> >>> Afsana >>> ______________________________ >>> *Afsana Afzal* >>> Clinical Research Coordinator >>> Massachusetts General Hospital >>> Division of Neurotherapeutics >>> Department of Psychiatry: Neurosciences >>> 149 13th St, Room 2612 >>> Charlestown, MA 02129 >>> Phone: 617-643-5129 >>> Fax: 617-726-4078 >>> ------------------------------ >>> *From:* Donald McLaren [[log in to unmask]] >>> *Sent:* Thursday, May 19, 2016 1:50 PM >>> *To:* Afzal, Afsana >>> *Cc:* [log in to unmask] >>> *Subject:* Re: [SPM] Changing fields in SPM.mat >>> >>> You can do that with spm_changepath. >>> >>> On May 19, 2016, at 10:55 AM, Afzal, Afsana >> > wrote: >>> >>> Hi everyone, >>> >>> Because of space constraints, I had to move my preprocessed data to a >>> different location. I'm trying to change the filepath information stored in >>> the SPM.mat files to reflect the location change. Is there an easy way to >>> iterate through the matfile and change all the paths (this would save me >>> from having to re-run all of my analyses). >>> >>> Thanks for your help, >>> >>> Afsana >>> >>> >>> ______________________________ >>> *Afsana Afzal* >>> Clinical Research Coordinator >>> Massachusetts General Hospital >>> Division of Neurotherapeutics >>> Department of Psychiatry: Neurosciences >>> 149 13th St, Room 2612 >>> Charlestown, MA 02129 >>> Phone: 617-643-5129 >>> Fax: 617-726-4078 >>> >>> 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 Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >> > > > -- > > ______________________________ > *Afsana Afzal* > Clinical Research Coordinator > Massachusetts General Hospital > Division of Neurotherapeutics > Department of Psychiatry: Neurosciences > 149 13th St, Room 2612 > Charlestown, MA 02129 > Phone: 617-643-5129 > Fax: 617-726-4078 > [log in to unmask] > ------------------------------ Date: Mon, 6 Jun 2016 15:49:03 -0400 From: "MCLAREN, Donald" Subject: Re: Introduction to Neuroimaging text Suggestions, in no particular order: Functional Magnetic Resonance Imaging, Scott Huettel Functional Magnetic Resonance Imaging: An Introduction to Methods, Peter Jezzard Handbook of Functional MRI Data Analysis, Russ Poldrack and Jeanette Mumford Best Regards, Donald McLaren, PhD On Mon, Jun 6, 2016 at 12:30 PM, Gaab, Nadine < [log in to unmask]> wrote: > Hi All, I would like to update readings for a class and I am looking for > some recommendations for good readings that cover a (very basic) > introduction to neuroimaging techniques (including the basics of MR > physics, the BOLD effect, experimental design, diffusion tensor imaging, > etc.). > > Does anyone have a good recommendation? > > Thank you. > > Nadine Gaab > > > > > > *"If we knew what it was we were doing, it would not be called research, > would it?" A. Einstein (1879-1955)* > > > > *Nadine Gaab, PhD* > > *Associate Professor of Pediatrics* > > *Boston Children's Hospital/Harvard Medical School * > > *Department of Medicine**/**Division of Developmental Medicine* > > *Laboratories of Cognitive Neuroscience* > > > *Mail stop code: BCH3178 1 Autumn Street (Office 643); Boston, MA 02115* > > *[log in to unmask] * > > *phone: 857-218-3021 * > > www.gaablab.com > > > ------------------------------ Date: Mon, 6 Jun 2016 16:09:52 -0400 From: "MCLAREN, Donald" Subject: Re: amyloid PET template Take a look at the following papers: http://www.ncbi.nlm.nih.gov/pubmed/18979777 http://www.ncbi.nlm.nih.gov/pubmed/24427295 Best Regards, Donald McLaren, PhD On Sun, Jun 5, 2016 at 3:37 AM, Gayane Aghakhanyan wrote: > Dear SPM community, > > I have limited amyloid PET data of two different groups of subjects, > unfortunately, without corresponding 3D T1 MRI data. Nonetheless, I'd like > to apply voxel-wise between group comparison of amyloid uptake by using an > amyloid PET template. Could some suggest me any useful sources where I can > find/ask/request an amyloid PET template to be used only for the research > proposes? > > Thank you beforehand, > > Gayane Aghakhanyan, MD, PhD > Resident Physician > University of Pisa, Department of Translational > Research and of New Surgical and Medical Technology > Tel: +393277013870 > email: [log in to unmask] > ------------------------------ Date: Mon, 6 Jun 2016 22:36:08 +0200 From: Manousos Klados Subject: Second Call for Papers Dear colleagues, please, accept our advanced apologies for any multiple cross-postings... The Society of Applied Neuroscience (SAN, http://www.applied-neuroscience.org/) in cooperation with the Medical School of the Aristotle University of Thessaloniki and the Department of Neurology of the Max Planck Institute for Human Cognitive and Brain Sciences, have the great pleasure to invite you to the biennial meeting of the Society, SAN2016 (http://applied-neuroscience.org/san2016/), which will be held in Corfu Island, Greece between 6-9 of October, 2016. We cordially invite everyone engaged in studies of Neuroscience, to participate in the SAN2016 meeting. Apart from the highly promising scientific program, blended with numerous workshops and special sessions, there will also be a lively social program which will give our guests the opportunity to enjoy Greece and Corfu.We feel confident than you will enjoy SAN2016 both scientifically and socially as one of our main purposes is to give the chance to all colleagues to establish new fruitful international collaborations in areas of mutual academic and clinical interests. SAN2016 will bring together scientists and practitioners from a wide range of specialist fields. These include, but are not limited to: EEG/ MEG/ fMRI/ fNIRS Neurofeedback fMRI-NFB studies Brain Computer Interfaces Trans Cranial Magnetic Stimulation Peripheral Biofeedback Direct Current Stimulation Event-Related Potentials Brain Connectivity Neuronal Reorganization EEG and Cognition QEEG Diagnosis Emerging combined EEG and Virtual/augmented reality technology Instrumentation Audio-Visual Stimulation LORETA & Methodology Clinical, educational, sport and optimal performance applications Rehabilitation Integrative Therapy Complimentary evidence-based applications ...and all fields of applied neuroscience. All the above blended by an attractive selection of keynote and invited speeches, as well as, hands-on pre-conference workshops. There will be a practitioner track focusing on topical issues. The conference committee receives more proposals than space available. Careful attention to Quality of work, clarity and completeness of the submitted materials is likely to increase the chance for acceptance. All the accepted abstracts will be published in the Frontiers in Human Neuroscience. SAN2016 abstract submission is supported by a Frontiers event and are directly submitted through the following link until the 20th of June, 2016: http://www.frontiersin.org/events/SAN2016_Meeting/3717 Numerous special issues and research topics are also planned by Society members as per tradition. We believe that SAN2016 will be a wonderful chance for you, to meet old friends and make new ones. We look forward to seeing you in Corfu, Greece! Panos Bamidis John Gruzelier Manousos Klados SAN2016 Conference Chairs [image: photo] *Manousos Klados, PhD* Postdoctoral Researcher, Max Planck Institute for Human Cognitive & Brain Sciences, +49(0)-341-9940-2507 | +49(0)-176-6988-1781 | http://www.mklados.com | Skype: mklados | Stephanstraße 1a PC D-04103 Leipzig Germany ----------------------------- *Call for Papers (Frontiers):*Applied Neuroscience: Methodology, Modeling, Theory, Applications and Reviews *Find me at* SAN2016 Conference ----------------------------- ------------------------------ Date: Mon, 6 Jun 2016 20:41:48 +0000 From: Sara Heyn Subject: Re: CAT12 Contrasts - 2x2 ANOVA Longitudinal Study Dear Christian, Thank you for your response! I think that interaction contrast makes sense. The problem I am running into now is that SPM is somehow not understanding sex as a covariate. The flexible factorial model requires that covariates be ordered as each subjects' scan back to back (so the first on the covariate vector would be subject 1 scan 1 code for sex, subject 1 scan 2 code for sex, subject 2 scan 1 code for sex... etc.) As such, the code for sex doesn't change over the two scans, so the list is a bunch of duplicate codes. I know it isn't working as it should because the contrast to just look at the main effect of sex is invalid - while I can look at the main effect of age and TIV just fine. Any ideas why sex would be causing such an issue? I have tried coding it as 0.5/-0.5, 1/0, and 1/-1, as well as both centering and not centering, and nothing has worked so far. To get around the issue, I tried taking out subject as a factor in the flexible factorial and taking out the main effect of subject in the model. Once I do that, sex doesn't seem to be an issue anymore. Is there something I am losing when I take out subject as a factor? Again, its a longitudinal 2x2 factorial, with 2 groups each getting 2 scans. All of the interactions seem to work this way, but I'm not sure what the effect of taking subject out is. Thanks in advance! Sara ________________________________ From: Christian Gaser Sent: Thursday, June 02, 2016 4:24:59 AM To: [log in to unmask]; Sara Heyn Cc: Christian Gaser Subject: Re: CAT12 Contrasts - 2x2 ANOVA Longitudinal Study Dear Sara, On Wed, 1 Jun 2016 20:58:35 +0100, Sara Heyn wrote: >Hi SPM Users, > >I have found a different way to model the group main effects suggested by Glascher & Gitelman (http://www.sbirc.ed.ac.uk/cyril/download/Contrast_Weighting_Glascher_Gitelman_2008.pdf) for my 2x2 longitudinal design. The contrast was: > >0.5 0.5 -0.5 -0.5 0 0 0 1/19 1/19 1/19 1/19 1/19 1/19 1/19 1/19 1/19 1/19 1/19 1/19 1/19 1/19 1/19 1/19 1/19 1/19 1/19 -1/22 -1/22 -1/22 -1/22 -1/22 -1/22 -1/22 -1/22 -1/22 -1/22 -1/22 -1/22 -1/22 -1/22 -1/22 -1/22 -1/22 -1/22 -1/22 -1/22 -1/22 -1/22 > >[The 0.5's are the 4 group*time interaction columns, followed by 3 covariates, and then 19 subjects in group 1 and 22 subjects in group 2] > >The contrast was valid, however the results that came back were huge (I used no masking, and a 0.05 FWE), on the order of a 60,000-voxel significant cluster. > >When I run time 1 and time 2 in separate t-tests, the effects come back MUCH smaller. Any ideas why there would be such a large discrepancy? > The contrast looks fine for me and I have also tested that with an own example and only find some smaller (meaningful) results. >RE: >I have built a flexible factorial design using CAT12 for two groups with two sessions (G1T1, G1T2, G2T1, G2T2) and I have a few questions about the contrasts to run. > >1. In the first model, I had 3 factors - subject, group, and time and did a main effect of subject, and an interaction effect of group x time. I am mostly interested in the interaction, so I ran an F-contrast and I just want to make sure it is actually modeling the interaction! I set it up as the following: > >1 -1 0 0 >-1 1 0 0 >0 0 1 -1 >0 0 -1 1 > This looks rather like an F-contrast for any time effects either in group one or two. If you are interested in the interaction you can try this: 1 -1 -1 1 There is no 2nd row for an F-test necessary with "-1 1 1 -1" because the direction is not tested, only the differences. Best, Christian >Does that look right? > >2. In that same model as in 1, I can get the main effect for time, but SPM is not letting me run a contrast to look at the main effect of group. So the t-contrasts for the time main effect (G1T1 > G2T2 "1 -1 0 0") was valid, but the t-contrast for group main effect (G1T1 > G2T1 "1 0 -1 0" or G1T2 > G2T2 "0 1 0 -1") is always invalid in the contrast manager. Any ideas why that would be? > >I also tried a different model, same as above by I added in the main effects for both group and time in the flexible factorial model. I attached the design matrix for that new model as well. The first two rows of the design matrix is just Group, so when I do a t-contrast for group ("1 -1") that is also invalid. > >Any help or ideas would be greatly appreciated! > >Thanks so much, > >Sara Heyn ------------------------------ End of SPM Digest - 5 Jun 2016 to 6 Jun 2016 (#2016-162) ********************************************************


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