Hi FreeSurfer users, I'm trying to use mri-preproc to do a group fMRI analysis(based on the tutorial). However, I keep getting an error that the number of input volumes does not equal number of subjects. It seems one volume is counted as 4 subjects. I'm wondering what the command determines to be the subject list when you use the --iv flag. For reference, I'm basing it off of this command: mris_preproc --target fsaverage --hemi lh \ --iv fbirn-101/ces.nii fbirn-101/bb.register.lta \ --iv fbirn-103/ces.nii fbirn-103/bb.register.lta \ --iv fbirn-104/ces.nii fbirn-104/bb.register.lta \ --iv fbirn-105/ces.nii fbirn-105/bb.register.lta \ --iv fbirn-106/ces.nii fbirn-106/bb.register.lta \ --projfrac 0.5 \ --out lh.ces.mgh Thanks! Talia
can you send the terminal output?
On 07/06/2016 11:32 AM, Raney, Talia L. wrote:
Hi FreeSurfer users, I'm trying to use mri-preproc to do a group fMRI analysis(based on the tutorial). However, I keep getting an error that the number of input volumes does not equal number of subjects. It seems one volume is counted as 4 subjects. I'm wondering what the command determines to be the subject list when you use the --iv flag. For reference, I'm basing it off of this command: mris_preproc --target fsaverage --hemi lh \ --iv fbirn-101/ces.nii fbirn-101/bb.register.lta \ --iv fbirn-103/ces.nii fbirn-103/bb.register.lta \ --iv fbirn-104/ces.nii fbirn-104/bb.register.lta \ --iv fbirn-105/ces.nii fbirn-105/bb.register.lta \ --iv fbirn-106/ces.nii fbirn-106/bb.register.lta \ --projfrac 0.5 \ --out lh.ces.mgh Thanks! Talia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
mris_preproc --target fsaverage --hemi lh --iv WADG77j/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz WADG77j/restingstate/bb.register.lta --iv WADG77k/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz WADG77k/restingstate/bb.register.lta --projfrac 0.5 --out lh.ces.mgh ERROR: number of input volumes (2) does not equal number of subjects (8) It apparently thinks one volume is 4 subjects but when checking bb.register.lta, it doesn't appear to be the case. Thanks! Talia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, July 06, 2016 1:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch
can you send the terminal output?
On 07/06/2016 11:32 AM, Raney, Talia L. wrote:
Hi FreeSurfer users, I'm trying to use mri-preproc to do a group fMRI analysis(based on the tutorial). However, I keep getting an error that the number of input volumes does not equal number of subjects. It seems one volume is counted as 4 subjects. I'm wondering what the command determines to be the subject list when you use the --iv flag. For reference, I'm basing it off of this command: mris_preproc --target fsaverage --hemi lh \ --iv fbirn-101/ces.nii fbirn-101/bb.register.lta \ --iv fbirn-103/ces.nii fbirn-103/bb.register.lta \ --iv fbirn-104/ces.nii fbirn-104/bb.register.lta \ --iv fbirn-105/ces.nii fbirn-105/bb.register.lta \ --iv fbirn-106/ces.nii fbirn-106/bb.register.lta \ --projfrac 0.5 \ --out lh.ces.mgh Thanks! Talia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It must be that one of the ces files has multiple frames. Try running mri_info --nframes ces.nii.gz on all of the ces files to see how many frames are in each
On 07/06/2016 01:39 PM, Raney, Talia L. wrote:
mris_preproc --target fsaverage --hemi lh --iv WADG77j/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz WADG77j/restingstate/bb.register.lta --iv WADG77k/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz WADG77k/restingstate/bb.register.lta --projfrac 0.5 --out lh.ces.mgh ERROR: number of input volumes (2) does not equal number of subjects (8) It apparently thinks one volume is 4 subjects but when checking bb.register.lta, it doesn't appear to be the case. Thanks! Talia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, July 06, 2016 1:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch
can you send the terminal output?
On 07/06/2016 11:32 AM, Raney, Talia L. wrote:
Hi FreeSurfer users, I'm trying to use mri-preproc to do a group fMRI analysis(based on the tutorial). However, I keep getting an error that the number of input volumes does not equal number of subjects. It seems one volume is counted as 4 subjects. I'm wondering what the command determines to be the subject list when you use the --iv flag. For reference, I'm basing it off of this command: mris_preproc --target fsaverage --hemi lh \ --iv fbirn-101/ces.nii fbirn-101/bb.register.lta \ --iv fbirn-103/ces.nii fbirn-103/bb.register.lta \ --iv fbirn-104/ces.nii fbirn-104/bb.register.lta \ --iv fbirn-105/ces.nii fbirn-105/bb.register.lta \ --iv fbirn-106/ces.nii fbirn-106/bb.register.lta \ --projfrac 0.5 \ --out lh.ces.mgh Thanks! Talia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hmm, it says that there is one frame in each of the subjects. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, July 06, 2016 1:54 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch
It must be that one of the ces files has multiple frames. Try running mri_info --nframes ces.nii.gz on all of the ces files to see how many frames are in each
On 07/06/2016 01:39 PM, Raney, Talia L. wrote:
mris_preproc --target fsaverage --hemi lh --iv WADG77j/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz WADG77j/restingstate/bb.register.lta --iv WADG77k/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz WADG77k/restingstate/bb.register.lta --projfrac 0.5 --out lh.ces.mgh ERROR: number of input volumes (2) does not equal number of subjects (8) It apparently thinks one volume is 4 subjects but when checking bb.register.lta, it doesn't appear to be the case. Thanks! Talia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, July 06, 2016 1:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch
can you send the terminal output?
On 07/06/2016 11:32 AM, Raney, Talia L. wrote:
Hi FreeSurfer users, I'm trying to use mri-preproc to do a group fMRI analysis(based on the tutorial). However, I keep getting an error that the number of input volumes does not equal number of subjects. It seems one volume is counted as 4 subjects. I'm wondering what the command determines to be the subject list when you use the --iv flag. For reference, I'm basing it off of this command: mris_preproc --target fsaverage --hemi lh \ --iv fbirn-101/ces.nii fbirn-101/bb.register.lta \ --iv fbirn-103/ces.nii fbirn-103/bb.register.lta \ --iv fbirn-104/ces.nii fbirn-104/bb.register.lta \ --iv fbirn-105/ces.nii fbirn-105/bb.register.lta \ --iv fbirn-106/ces.nii fbirn-106/bb.register.lta \ --projfrac 0.5 \ --out lh.ces.mgh Thanks! Talia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Ah, the problem is with using an lta with 5.3 mris_preproc. I've put version 6 mris_preproc here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc try that and see if it works. Alternatively, you could convert the lta files to register.dat files
On 07/06/2016 02:02 PM, Raney, Talia L. wrote:
Hmm, it says that there is one frame in each of the subjects. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, July 06, 2016 1:54 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch
It must be that one of the ces files has multiple frames. Try running mri_info --nframes ces.nii.gz on all of the ces files to see how many frames are in each
On 07/06/2016 01:39 PM, Raney, Talia L. wrote:
mris_preproc --target fsaverage --hemi lh --iv WADG77j/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz WADG77j/restingstate/bb.register.lta --iv WADG77k/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz WADG77k/restingstate/bb.register.lta --projfrac 0.5 --out lh.ces.mgh ERROR: number of input volumes (2) does not equal number of subjects (8) It apparently thinks one volume is 4 subjects but when checking bb.register.lta, it doesn't appear to be the case. Thanks! Talia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, July 06, 2016 1:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch
can you send the terminal output?
On 07/06/2016 11:32 AM, Raney, Talia L. wrote:
Hi FreeSurfer users, I'm trying to use mri-preproc to do a group fMRI analysis(based on the tutorial). However, I keep getting an error that the number of input volumes does not equal number of subjects. It seems one volume is counted as 4 subjects. I'm wondering what the command determines to be the subject list when you use the --iv flag. For reference, I'm basing it off of this command: mris_preproc --target fsaverage --hemi lh \ --iv fbirn-101/ces.nii fbirn-101/bb.register.lta \ --iv fbirn-103/ces.nii fbirn-103/bb.register.lta \ --iv fbirn-104/ces.nii fbirn-104/bb.register.lta \ --iv fbirn-105/ces.nii fbirn-105/bb.register.lta \ --iv fbirn-106/ces.nii fbirn-106/bb.register.lta \ --projfrac 0.5 \ --out lh.ces.mgh Thanks! Talia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It worked with the register.dat files. Thank you! ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, July 06, 2016 2:07 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch
Ah, the problem is with using an lta with 5.3 mris_preproc. I've put version 6 mris_preproc here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc try that and see if it works. Alternatively, you could convert the lta files to register.dat files
On 07/06/2016 02:02 PM, Raney, Talia L. wrote:
Hmm, it says that there is one frame in each of the subjects. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, July 06, 2016 1:54 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch
It must be that one of the ces files has multiple frames. Try running mri_info --nframes ces.nii.gz on all of the ces files to see how many frames are in each
On 07/06/2016 01:39 PM, Raney, Talia L. wrote:
mris_preproc --target fsaverage --hemi lh --iv WADG77j/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz WADG77j/restingstate/bb.register.lta --iv WADG77k/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz WADG77k/restingstate/bb.register.lta --projfrac 0.5 --out lh.ces.mgh ERROR: number of input volumes (2) does not equal number of subjects (8) It apparently thinks one volume is 4 subjects but when checking bb.register.lta, it doesn't appear to be the case. Thanks! Talia ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Wednesday, July 06, 2016 1:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch
can you send the terminal output?
On 07/06/2016 11:32 AM, Raney, Talia L. wrote:
Hi FreeSurfer users, I'm trying to use mri-preproc to do a group fMRI analysis(based on the tutorial). However, I keep getting an error that the number of input volumes does not equal number of subjects. It seems one volume is counted as 4 subjects. I'm wondering what the command determines to be the subject list when you use the --iv flag. For reference, I'm basing it off of this command: mris_preproc --target fsaverage --hemi lh \ --iv fbirn-101/ces.nii fbirn-101/bb.register.lta \ --iv fbirn-103/ces.nii fbirn-103/bb.register.lta \ --iv fbirn-104/ces.nii fbirn-104/bb.register.lta \ --iv fbirn-105/ces.nii fbirn-105/bb.register.lta \ --iv fbirn-106/ces.nii fbirn-106/bb.register.lta \ --projfrac 0.5 \ --out lh.ces.mgh Thanks! Talia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Raney, Talia L.