Hi Reem,
Did you use the -o option in cluster to get a cluster Index map? You should Be able to go from there to seperate the two.
Cheers,
Andreas
________________________________________
Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von Reem Jan [[log in to unmask]]
Gesendet: Donnerstag, 16. Dezember 2010 21:28
An: [log in to unmask]
Betreff: Re: [FSL] AW: Is there an FSL-VBM for longitudinal studies yet?
Hi Andreas
Thank you for that. Yes I have tried the cluster command and was able to
obtain the X Y Z co-ordinates of all the significant clusters as an
output.
I followed these steps:
1. cluster --in= fslvbms3_tfce_corrp_tstat1 --thresh=0.949 --mm
The output was two significant clusters and their co-ordinates
2. fslmaths fslvbms3_tfce_corrp_tstat1.nii.gz -thr 0.949 -bin mask_
fslvbms3_tfce_corrp_tstat1
The output was a mask of the two significant clusters (I'm only
interested in one of these clusters for quantification of GM volume)
3. fslmeants -i GM_mod_merg_s3.nii.gz -m mask_
fslvbms3_tfce_corrp_tstat1 -o mean_GM_density.txt
The output was a text file of 1 x GM density value per subject (i.e.
this is a mean GM density value of both clusters).
But I wasn't sure how to use fslmaths to make a mask of just the one
cluster I was interested in?
Many thanks for your help and I hope your Christmas preparations are
going well!
Cheers
Reem
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
Behalf Of Andreas Bartsch
Sent: Thursday, December 16, 2010 8:00 PM
To: [log in to unmask]
Subject: [FSL] AW: Is there an FSL-VBM for longitudinal studies yet?
Hi Reem,
Not yet - but Gwen is working on it and it is supposed to be in the next
release.
For the other part: have you tried 'cluster'?
cheers,
Andreas
________________________________________
Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von
Reem Jan [[log in to unmask]]
Gesendet: Donnerstag, 16. Dezember 2010 04:11
An: [log in to unmask]
Betreff: [FSL] Is there an FSL-VBM for longitudinal studies yet?
Dear FSLers
Can someone please let me know whether the FSL-VBM tool for analyzing a
longitudinal VBM study is available yet?
Also I am stuck on how to use fslmaths to make a mask of only 1
activation cluster at a time from a tstat map (from VBM results) which
contains more than 1 significant cluster. I tried many of the options in
fslmaths but couldn't figure out, any suggestions would be greatly
appreciated.
Many thanks
Reem
__________ Information from ESET NOD32 Antivirus, version of virus
signature database 5706 (20101215) __________
The message was checked by ESET NOD32 Antivirus.
http://www.eset.com
__________ Information from ESET NOD32 Antivirus, version of virus
signature database 5708 (20101216) __________
The message was checked by ESET NOD32 Antivirus.
http://www.eset.com
__________ Information from ESET NOD32 Antivirus, version of virus
signature database 5708 (20101216) __________
The message was checked by ESET NOD32 Antivirus.
http://www.eset.com
|