Hi,
I'm doing first level analysis in FSFAST and I'm consistently getting the following error when running fast_selxavg3():
Saving to /autofs/space/lilli_002/users/DARPA-FAST/hc016/msit/msit.analysis.sm04.b0dc.mni305/rho1mn.sm.nii.gz SmoothOnly requested, so exiting now
Found 0 voxels with corrected AR1 > 0.90 Whitening Attempted to access indedge(0); index must be a positive integer or logical.
Error in fast_histeq (line 53) if(indedge(end) ~= ny) indedge = [indedge ny]; end
Error in fast_selxavg3 (line 640) [edge bincenter binmap] = fast_histeq(nrho1mn.vol(indmask), flac0.acfbins);
ERROR: fast_selxavg3() failed\n
I'm only getting the error for mni305 (lh and rh analyses are completing without a hitch). I have re-preprocessed and attempted to run the analysis several times, but without any success. It's not clear what the error means or what's causing it.
Thank you for any 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
hmmm, not sure. Can you send me your selxavg3-sess command and the folder your ran it from and the $SUBJECTS_DIR ? doug
On 11/13/15 4:16 PM, Afzal, Afsana wrote:
Hi,
I'm doing first level analysis in FSFAST and I'm consistently getting the following error when running fast_selxavg3():
Saving to /autofs/space/lilli_002/users/DARPA-FAST/hc016/msit/msit.analysis.sm04.b0dc.mni305/rho1mn.sm.nii.gz SmoothOnly requested, so exiting now
Found 0 voxels with corrected AR1 > 0.90 Whitening Attempted to access indedge(0); index must be a positive integer or logical.
Error in fast_histeq (line 53) if(indedge(end) ~= ny) indedge = [indedge ny]; end
Error in fast_selxavg3 (line 640) [edge bincenter binmap] = fast_histeq(nrho1mn.vol(indmask), flac0.acfbins);
ERROR: fast_selxavg3() failed\n
I'm only getting the error for mni305 (lh and rh analyses are completing without a hitch). I have re-preprocessed and attempted to run the analysis several times, but without any success. It's not clear what the error means or what's causing it.
Thank you for any 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Command: selxavg3-sess -s hc016 -analysis msit.analysis.sm04.b0dc.mni305 -force Folder: /autofs/space/lilli_002/users/DARPA-FAST $SUBJECTS_DIR: /autofs/space/lilli_001/users/DARPA-MEG/freesurfs
The problem might actually lie with preprocessing.
Just looking at file sizes, the fmcpr.sm4.mni305.2mm.b0dc.nii.gz file size for hc016 is 471kb, but it's ~46mb for other subjects. The lh and rh files for hc016 are also pretty small compared to other subjects. Not sure what's causing this.
This is the preproc command I used: preproc-sess -s hc016 -surface fsaverage lhrh -mni305 -fwhm 4 -per-run -fsd msit -nostc -b0dc -force
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 ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, November 13, 2015 5:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR
hmmm, not sure. Can you send me your selxavg3-sess command and the folder your ran it from and the $SUBJECTS_DIR ? doug
On 11/13/15 4:16 PM, Afzal, Afsana wrote: Hi,
I'm doing first level analysis in FSFAST and I'm consistently getting the following error when running fast_selxavg3():
Saving to /autofs/space/lilli_002/users/DARPA-FAST/hc016/msit/msit.analysis.sm04.b0dc.mni305/rho1mn.sm.nii.gz SmoothOnly requested, so exiting now
Found 0 voxels with corrected AR1 > 0.90 Whitening Attempted to access indedge(0); index must be a positive integer or logical.
Error in fast_histeq (line 53) if(indedge(end) ~= ny) indedge = [indedge ny]; end
Error in fast_selxavg3 (line 640) [edge bincenter binmap] = fast_histeq(nrho1mn.vol(indmask), flac0.acfbins);
ERROR: fast_selxavg3() failed\n
I'm only getting the error for mni305 (lh and rh analyses are completing without a hitch). I have re-preprocessed and attempted to run the analysis several times, but without any success. It's not clear what the error means or what's causing it.
Thank you for any 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
When I look in hc016/msit/001/ I only see:
cfg.txt f.nii mag.dat mag.nii phase.dat phase.nii
Have you deleted the previous analysis?
On 11/16/2015 11:41 AM, Afzal, Afsana wrote:
Hi Doug,
Command: selxavg3-sess -s hc016 -analysis msit.analysis.sm04.b0dc.mni305 -force Folder: /autofs/space/lilli_002/users/DARPA-FAST $SUBJECTS_DIR: /autofs/space/lilli_001/users/DARPA-MEG/freesurfs
The problem might actually lie with preprocessing.
Just looking at file sizes, the fmcpr.sm4.mni305.2mm.b0dc.nii.gz file size for hc016 is 471kb, but it's ~46mb for other subjects. The lh and rh files for hc016 are also pretty small compared to other subjects. Not sure what's causing this.
This is the preproc command I used: preproc-sess -s hc016 -surface fsaverage lhrh -mni305 -fwhm 4 -per-run -fsd msit -nostc -b0dc -force
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
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] *Sent:* Friday, November 13, 2015 5:04 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR
hmmm, not sure. Can you send me your selxavg3-sess command and the folder your ran it from and the $SUBJECTS_DIR ? doug
On 11/13/15 4:16 PM, Afzal, Afsana wrote:
Hi,
I'm doing first level analysis in FSFAST and I'm consistently getting the following error when running fast_selxavg3():
Saving to /autofs/space/lilli_002/users/DARPA-FAST/hc016/msit/msit.analysis.sm04.b0dc.mni305/rho1mn.sm.nii.gz SmoothOnly requested, so exiting now
Found 0 voxels with corrected AR1 > 0.90 Whitening Attempted to access indedge(0); index must be a positive integer or logical.
Error in fast_histeq (line 53) if(indedge(end) ~= ny) indedge = [indedge ny]; end
Error in fast_selxavg3 (line 640) [edge bincenter binmap] = fast_histeq(nrho1mn.vol(indmask), flac0.acfbins);
ERROR: fast_selxavg3() failed\n
I'm only getting the error for mni305 (lh and rh analyses are completing without a hitch). I have re-preprocessed and attempted to run the analysis several times, but without any success. It's not clear what the error means or what's causing it.
Thank you for any 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
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
Yeah sorry, I was rerunning the preproc. Should be there now.
______________________________ 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: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, November 16, 2015 12:48 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR
When I look in hc016/msit/001/ I only see:
cfg.txt f.nii mag.dat mag.nii phase.dat phase.nii
Have you deleted the previous analysis?
On 11/16/2015 11:41 AM, Afzal, Afsana wrote:
Hi Doug,
Command: selxavg3-sess -s hc016 -analysis msit.analysis.sm04.b0dc.mni305 -force Folder: /autofs/space/lilli_002/users/DARPA-FAST $SUBJECTS_DIR: /autofs/space/lilli_001/users/DARPA-MEG/freesurfs
The problem might actually lie with preprocessing.
Just looking at file sizes, the fmcpr.sm4.mni305.2mm.b0dc.nii.gz file size for hc016 is 471kb, but it's ~46mb for other subjects. The lh and rh files for hc016 are also pretty small compared to other subjects. Not sure what's causing this.
This is the preproc command I used: preproc-sess -s hc016 -surface fsaverage lhrh -mni305 -fwhm 4 -per-run -fsd msit -nostc -b0dc -force
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
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] *Sent:* Friday, November 13, 2015 5:04 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR
hmmm, not sure. Can you send me your selxavg3-sess command and the folder your ran it from and the $SUBJECTS_DIR ? doug
On 11/13/15 4:16 PM, Afzal, Afsana wrote:
Hi,
I'm doing first level analysis in FSFAST and I'm consistently getting the following error when running fast_selxavg3():
Saving to /autofs/space/lilli_002/users/DARPA-FAST/hc016/msit/msit.analysis.sm04.b0dc.mni305/rho1mn.sm.nii.gz SmoothOnly requested, so exiting now
Found 0 voxels with corrected AR1 > 0.90 Whitening Attempted to access indedge(0); index must be a positive integer or logical.
Error in fast_histeq (line 53) if(indedge(end) ~= ny) indedge = [indedge ny]; end
Error in fast_selxavg3 (line 640) [edge bincenter binmap] = fast_histeq(nrho1mn.vol(indmask), flac0.acfbins);
ERROR: fast_selxavg3() failed\n
I'm only getting the error for mni305 (lh and rh analyses are completing without a hitch). I have re-preprocessed and attempted to run the analysis several times, but without any success. It's not clear what the error means or what's causing it.
Thank you for any 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
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
Hi Doug,
Just checking up on the error below.
______________________________ 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: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana [AAFZAL@mgh.harvard.edu] Sent: Monday, November 16, 2015 2:14 PM To: Freesurfer support list Subject: Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR
Yeah sorry, I was rerunning the preproc. Should be there now.
______________________________ 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: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, November 16, 2015 12:48 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR
When I look in hc016/msit/001/ I only see:
cfg.txt f.nii mag.dat mag.nii phase.dat phase.nii
Have you deleted the previous analysis?
On 11/16/2015 11:41 AM, Afzal, Afsana wrote:
Hi Doug,
Command: selxavg3-sess -s hc016 -analysis msit.analysis.sm04.b0dc.mni305 -force Folder: /autofs/space/lilli_002/users/DARPA-FAST $SUBJECTS_DIR: /autofs/space/lilli_001/users/DARPA-MEG/freesurfs
The problem might actually lie with preprocessing.
Just looking at file sizes, the fmcpr.sm4.mni305.2mm.b0dc.nii.gz file size for hc016 is 471kb, but it's ~46mb for other subjects. The lh and rh files for hc016 are also pretty small compared to other subjects. Not sure what's causing this.
This is the preproc command I used: preproc-sess -s hc016 -surface fsaverage lhrh -mni305 -fwhm 4 -per-run -fsd msit -nostc -b0dc -force
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
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] *Sent:* Friday, November 13, 2015 5:04 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR
hmmm, not sure. Can you send me your selxavg3-sess command and the folder your ran it from and the $SUBJECTS_DIR ? doug
On 11/13/15 4:16 PM, Afzal, Afsana wrote:
Hi,
I'm doing first level analysis in FSFAST and I'm consistently getting the following error when running fast_selxavg3():
Saving to /autofs/space/lilli_002/users/DARPA-FAST/hc016/msit/msit.analysis.sm04.b0dc.mni305/rho1mn.sm.nii.gz SmoothOnly requested, so exiting now
Found 0 voxels with corrected AR1 > 0.90 Whitening Attempted to access indedge(0); index must be a positive integer or logical.
Error in fast_histeq (line 53) if(indedge(end) ~= ny) indedge = [indedge ny]; end
Error in fast_selxavg3 (line 640) [edge bincenter binmap] = fast_histeq(nrho1mn.vol(indmask), flac0.acfbins);
ERROR: fast_selxavg3() failed\n
I'm only getting the error for mni305 (lh and rh analyses are completing without a hitch). I have re-preprocessed and attempted to run the analysis several times, but without any success. It's not clear what the error means or what's causing it.
Thank you for any 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
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
The problem is that the registration is bad. You can get a measure of the quality of the registration with
tkregister-sess -s hc016 -per-run -bbr-sum bbrcost.dat -fsd msit -b0dc
The cost for this subject was 0.9859, which is pretty bad. The values for the other subjects are below. You can see that most are less than 0.4. There are 4 that are more than .79. These are all probably bad. Probably due to a bad initial registration as created by FSL. You can try re-running these subjects using preproc-sess -init-spm ... The SPM registration is much more robust than the FSL but needs matlab (and spm). Let me know if that fixes the problem.
For version 6, I have a new program that I wrote (mri_coreg) which basically replicates spm_coreg but is native to FS and does not need matlab. Version 6 registration will use this by default.
doug
hc022 001 0.2072 hc015 001 0.2078 pp001 001 0.2328 pp008 001 0.2350 hc014 001 0.2412 pp005 001 0.2415 hc013 001 0.2462 pp009 001 0.2467 pp004 001 0.2570 hc020 001 0.2577 hc021 001 0.2699 pp003 001 0.2753 hc008 001 0.2828 hc001 001 0.2855 hc019 001 0.2915 hc023 001 0.3002 hc011 001 0.3032 pp010 001 0.3048 hc005 001 0.3052 hc006 001 0.3097 hc004 001 0.3115 hc010 001 0.3136 hc018 001 0.3155 hc003 001 0.3228 hc007 001 0.3248 hc017 001 0.3366 pp007 001 0.3425 hc009 001 0.3616 hc012 001 0.3748 hc002 001 0.7959 pp006 001 0.8398 pp002 001 0.8801 hc016 001 0.9859
On 11/18/15 1:17 PM, Afzal, Afsana wrote:
Hi Doug,
Just checking up on the error below.
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: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana [AAFZAL@mgh.harvard.edu] Sent: Monday, November 16, 2015 2:14 PM To: Freesurfer support list Subject: Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR
Yeah sorry, I was rerunning the preproc. Should be there now.
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: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, November 16, 2015 12:48 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR
When I look in hc016/msit/001/ I only see:
cfg.txt f.nii mag.dat mag.nii phase.dat phase.nii
Have you deleted the previous analysis?
On 11/16/2015 11:41 AM, Afzal, Afsana wrote:
Hi Doug,
Command: selxavg3-sess -s hc016 -analysis msit.analysis.sm04.b0dc.mni305 -force Folder: /autofs/space/lilli_002/users/DARPA-FAST $SUBJECTS_DIR: /autofs/space/lilli_001/users/DARPA-MEG/freesurfs
The problem might actually lie with preprocessing.
Just looking at file sizes, the fmcpr.sm4.mni305.2mm.b0dc.nii.gz file size for hc016 is 471kb, but it's ~46mb for other subjects. The lh and rh files for hc016 are also pretty small compared to other subjects. Not sure what's causing this.
This is the preproc command I used: preproc-sess -s hc016 -surface fsaverage lhrh -mni305 -fwhm 4 -per-run -fsd msit -nostc -b0dc -force
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
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] *Sent:* Friday, November 13, 2015 5:04 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] FSFAST First-Levels: Fast_selxavg3() ERROR
hmmm, not sure. Can you send me your selxavg3-sess command and the folder your ran it from and the $SUBJECTS_DIR ? doug
On 11/13/15 4:16 PM, Afzal, Afsana wrote:
Hi,
I'm doing first level analysis in FSFAST and I'm consistently getting the following error when running fast_selxavg3():
Saving to /autofs/space/lilli_002/users/DARPA-FAST/hc016/msit/msit.analysis.sm04.b0dc.mni305/rho1mn.sm.nii.gz SmoothOnly requested, so exiting now
Found 0 voxels with corrected AR1 > 0.90 Whitening Attempted to access indedge(0); index must be a positive integer or logical.
Error in fast_histeq (line 53) if(indedge(end) ~= ny) indedge = [indedge ny]; end
Error in fast_selxavg3 (line 640) [edge bincenter binmap] = fast_histeq(nrho1mn.vol(indmask), flac0.acfbins);
ERROR: fast_selxavg3() failed\n
I'm only getting the error for mni305 (lh and rh analyses are completing without a hitch). I have re-preprocessed and attempted to run the analysis several times, but without any success. It's not clear what the error means or what's causing it.
Thank you for any 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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Afzal, Afsana -
Douglas Greve -
Douglas N Greve