Thanks for the reply Doug. This is content of my mri_glmfit.log:

--------------------------------------------------------------------------------------------------- $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /home/adits123/Desktop/projectoutputdata cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh sysname Linux hostname localhost.localdomain machine x86_64 user adits123 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh logyflag 0 usedti 0 FSGD paireddifftp1tp2.txt labelmask /home/adits123/Desktop/projectoutputdata/fsaverage/label/rh.cortex.label maskinv 0 glmdir rh.paired-diff.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 ResidualFWHM -nan SearchSpace 32101.581527 anattype surface ---------------------------------------------------------------------------------------------------------

The left hemisphere says pretty much the same thing, with the ResidualFWHM 0.000000 and SearchSpace 44094.721767

Thanks Koushik

_______________________________________ 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: Friday, May 06, 2016 10:46 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim error

The problem is with the estimate of the FWHM for that run. Can you re-run mri_glmfit and send me the command line and terminal output?

On 05/06/2016 10:27 AM, Govindarajan, Koushik Athreya wrote:

Dear FS experts,

    I ran into an error with one of my mri_glmfit-sim execution

and was not sure what was going on. The same simulation is currently running for the left hemisphere without any hiccups but I get this following error for the right hemisphere:

---

cd /home/adits123/Desktop/projectoutputdata /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir --sim mc-z 10000 1.3 mc-z.pos.1.3 --sim-sign pos --cwpvalthresh 0.05

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Thu May 5 13:16:51 CDT 2016 Linux localhost.localdomain 2.6.32-250.el6.x86_64 #1 SMP Tue Mar 6 23:00:19 EST 2012 x86_64 x86_64 x86_64 GNU/Linux adits123 setenv SUBJECTS_DIR /home/adits123/Desktop/projectoutputdata FREESURFER_HOME /usr/local/freesurfer

Original mri_glmfit command line: cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh

DoSim = 1 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = -nan nSimPerJob = 10000 1/1 Thu May 5 13:16:51 CDT 2016 mri_glmfit --y /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh --C /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/tmp.mri_glmfit-sim-931/contrastpaired.mtx --mask /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/mask.mgh --sim mc-z 10000 1.3 /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001 --sim-sign pos --fwhm -nan --fsgd /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/y.fsgd dods --surf fsaverage rh white simbase /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001 FWHM = -nan ERROR: input FWHM is NaN (not a number). Check the mask in the glm directory. Thu May 5 13:16:51 CDT 2016 ERROR: cannot find any csd files

---

I am not sure what the fwhm is NaN error is and also why it is only showing up for one hemisphere. Any help is appreciated.

Thanks Koushik Govindarajan

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...

-- 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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed... www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...

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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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.

This is the command line output for mri_glmfit:

------------------------------------------------------------------------------------------------------------------------ [adits123@localhost projectoutputdata]$ mri_glmfit --glmdir rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh gdfReadHeader: reading paireddifftp1tp2.txt INFO: gd2mtx_method is dods Reading source surface /home/adits123/Desktop/projectoutputdata/fsaverage/surf/rh.white Number of vertices 163842 Number of faces 327680 Total area 65020.765625 AvgVtxArea 0.396850 AvgVtxDist 0.717994 StdVtxDist 0.193566

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /home/adits123/Desktop/projectoutputdata cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh sysname Linux hostname localhost.localdomain machine x86_64 user adits123 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh logyflag 0 usedti 0 FSGD paireddifftp1tp2.txt labelmask /home/adits123/Desktop/projectoutputdata/fsaverage/label/rh.cortex.label maskinv 0 glmdir rh.paired-diff.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory rh.paired-diff.glmdir Loading y from /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh INFO: gd2mtx_method is dods Saving design matrix to rh.paired-diff.glmdir/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 149926 points in label. Pruning voxels by thr: 0.000000 Found 65950 voxels in mask Saving mask to rh.paired-diff.glmdir/mask.mgh Reshaping mriglm->mask... search space = 32101.581527 DOF = 364 Starting fit and test Fit completed in 0.03265 minutes Computing spatial AR1 on surface Residual: ar1mn=inf, ar1std=-nan, gstd=-nan, fwhm=-nan Writing results contrastpaired maxvox sig=4.51832 F=17.8453 at index 50390 0 0 seed=1463164810 mri_glmfit done

---------------------------------------------------------------------------------------------------------------------------

This is mri_glmfit-sim: --------------------------------------------------------------------------------------------------------------------------- [adits123@localhost projectoutputdata]$ mri_glmfit-sim --glmdir $SUBJECTS_DIR/rh.paired-diff.glmdir --sim mc-z 10000 1.3 mc-z.pos.1.3 --sim-sign pos --cwpvalthresh 0.05 cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh SURFACE: fsaverage rh log file is /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/mc-z.pos.1.3.mri_glmfit-sim.log

cd /home/adits123/Desktop/projectoutputdata /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir --sim mc-z 10000 1.3 mc-z.pos.1.3 --sim-sign pos --cwpvalthresh 0.05

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Mon May 9 09:11:28 CDT 2016 Linux localhost.localdomain 2.6.32-250.el6.x86_64 #1 SMP Tue Mar 6 23:00:19 EST 2012 x86_64 x86_64 x86_64 GNU/Linux adits123 setenv SUBJECTS_DIR /home/adits123/Desktop/projectoutputdata FREESURFER_HOME /usr/local/freesurfer

Original mri_glmfit command line: cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh

DoSim = 1 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = -nan nSimPerJob = 10000 1/1 Mon May 9 09:11:28 CDT 2016 mri_glmfit --y /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh --C /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/tmp.mri_glmfit-sim-11863/contrastpaired.mtx --mask /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/mask.mgh --sim mc-z 10000 1.3 /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001 --sim-sign pos --fwhm -nan --fsgd /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/y.fsgd dods --surf fsaverage rh white simbase /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001 FWHM = -nan ERROR: input FWHM is NaN (not a number). Check the mask in the glm directory. Mon May 9 09:11:28 CDT 2016 ERROR: cannot find any csd files

---------------------------------------------------------------------------------------------------------------------

Many thanks for helping me with this Doug.

Regards Koushik

________________________________________ 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: Friday, May 06, 2016 3:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim error

something is going wrong because the FWHM is not-a-number (nan). Can you send the actual terminal output and not just the log file?

On 05/06/2016 11:55 AM, Govindarajan, Koushik Athreya wrote:

Thanks for the reply Doug. This is content of my mri_glmfit.log:

---

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /home/adits123/Desktop/projectoutputdata cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh sysname Linux hostname localhost.localdomain machine x86_64 user adits123 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh logyflag 0 usedti 0 FSGD paireddifftp1tp2.txt labelmask /home/adits123/Desktop/projectoutputdata/fsaverage/label/rh.cortex.label maskinv 0 glmdir rh.paired-diff.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 ResidualFWHM -nan SearchSpace 32101.581527 anattype surface

---

The left hemisphere says pretty much the same thing, with the ResidualFWHM 0.000000 and SearchSpace 44094.721767

Thanks Koushik

---

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: Friday, May 06, 2016 10:46 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim error

The problem is with the estimate of the FWHM for that run. Can you re-run mri_glmfit and send me the command line and terminal output?

On 05/06/2016 10:27 AM, Govindarajan, Koushik Athreya wrote:

...

Dear FS experts,

     I ran into an error with one of my mri_glmfit-sim execution

and was not sure what was going on. The same simulation is currently running for the left hemisphere without any hiccups but I get this following error for the right hemisphere:

---

cd /home/adits123/Desktop/projectoutputdata /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir --sim mc-z 10000 1.3 mc-z.pos.1.3 --sim-sign pos --cwpvalthresh 0.05

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Thu May 5 13:16:51 CDT 2016 Linux localhost.localdomain 2.6.32-250.el6.x86_64 #1 SMP Tue Mar 6 23:00:19 EST 2012 x86_64 x86_64 x86_64 GNU/Linux adits123 setenv SUBJECTS_DIR /home/adits123/Desktop/projectoutputdata FREESURFER_HOME /usr/local/freesurfer

Original mri_glmfit command line: cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh

DoSim = 1 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = -nan nSimPerJob = 10000 1/1 Thu May 5 13:16:51 CDT 2016 mri_glmfit --y /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh --C /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/tmp.mri_glmfit-sim-931/contrastpaired.mtx --mask /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/mask.mgh --sim mc-z 10000 1.3 /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001 --sim-sign pos --fwhm -nan --fsgd /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/y.fsgd dods --surf fsaverage rh white simbase /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001 FWHM = -nan ERROR: input FWHM is NaN (not a number). Check the mask in the glm directory. Thu May 5 13:16:51 CDT 2016 ERROR: cannot find any csd files

---

I am not sure what the fwhm is NaN error is and also why it is only showing up for one hemisphere. Any help is appreciated.

Thanks Koushik Govindarajan

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...

-- 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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed... www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...

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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...

-- 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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed... www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...

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 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complia... . 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.

First did the mris_preproc and then the mri_surf2surf. Followed the group analysis wiki basically.

Thanks Koushik

________________________________________ 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, May 09, 2016 5:30 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim error

It looks like over half your voxels have been pruned because they have value identical to 0 in at least one subject

Found 149926 points in label. Pruning voxels by thr: 0.000000 Found 65950 voxels in mask

How did you create rh.paired-diff.thickness.sm05.mgh?

On 05/09/2016 10:24 AM, Govindarajan, Koushik Athreya wrote:

This is the command line output for mri_glmfit:

---

[adits123@localhost projectoutputdata]$ mri_glmfit --glmdir rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh gdfReadHeader: reading paireddifftp1tp2.txt INFO: gd2mtx_method is dods Reading source surface /home/adits123/Desktop/projectoutputdata/fsaverage/surf/rh.white Number of vertices 163842 Number of faces 327680 Total area 65020.765625 AvgVtxArea 0.396850 AvgVtxDist 0.717994 StdVtxDist 0.193566

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /home/adits123/Desktop/projectoutputdata cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh sysname Linux hostname localhost.localdomain machine x86_64 user adits123 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh logyflag 0 usedti 0 FSGD paireddifftp1tp2.txt labelmask /home/adits123/Desktop/projectoutputdata/fsaverage/label/rh.cortex.label maskinv 0 glmdir rh.paired-diff.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory rh.paired-diff.glmdir Loading y from /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh INFO: gd2mtx_method is dods Saving design matrix to rh.paired-diff.glmdir/Xg.dat Normalized matrix condition is 1 Matrix condition is 1 Found 149926 points in label. Pruning voxels by thr: 0.000000 Found 65950 voxels in mask Saving mask to rh.paired-diff.glmdir/mask.mgh Reshaping mriglm->mask... search space = 32101.581527 DOF = 364 Starting fit and test Fit completed in 0.03265 minutes Computing spatial AR1 on surface Residual: ar1mn=inf, ar1std=-nan, gstd=-nan, fwhm=-nan Writing results contrastpaired maxvox sig=4.51832 F=17.8453 at index 50390 0 0 seed=1463164810 mri_glmfit done

---

This is mri_glmfit-sim:

[adits123@localhost projectoutputdata]$ mri_glmfit-sim --glmdir $SUBJECTS_DIR/rh.paired-diff.glmdir --sim mc-z 10000 1.3 mc-z.pos.1.3 --sim-sign pos --cwpvalthresh 0.05 cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh SURFACE: fsaverage rh log file is /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/mc-z.pos.1.3.mri_glmfit-sim.log

cd /home/adits123/Desktop/projectoutputdata /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir --sim mc-z 10000 1.3 mc-z.pos.1.3 --sim-sign pos --cwpvalthresh 0.05

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Mon May 9 09:11:28 CDT 2016 Linux localhost.localdomain 2.6.32-250.el6.x86_64 #1 SMP Tue Mar 6 23:00:19 EST 2012 x86_64 x86_64 x86_64 GNU/Linux adits123 setenv SUBJECTS_DIR /home/adits123/Desktop/projectoutputdata FREESURFER_HOME /usr/local/freesurfer

Original mri_glmfit command line: cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh

DoSim = 1 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = -nan nSimPerJob = 10000 1/1 Mon May 9 09:11:28 CDT 2016 mri_glmfit --y /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh --C /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/tmp.mri_glmfit-sim-11863/contrastpaired.mtx --mask /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/mask.mgh --sim mc-z 10000 1.3 /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001 --sim-sign pos --fwhm -nan --fsgd /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/y.fsgd dods --surf fsaverage rh white simbase /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001 FWHM = -nan ERROR: input FWHM is NaN (not a number). Check the mask in the glm directory. Mon May 9 09:11:28 CDT 2016 ERROR: cannot find any csd files

---

Many thanks for helping me with this Doug.

Regards Koushik

---

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: Friday, May 06, 2016 3:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim error

something is going wrong because the FWHM is not-a-number (nan). Can you send the actual terminal output and not just the log file?

On 05/06/2016 11:55 AM, Govindarajan, Koushik Athreya wrote:

...

Thanks for the reply Doug. This is content of my mri_glmfit.log:

---

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /home/adits123/Desktop/projectoutputdata cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh sysname Linux hostname localhost.localdomain machine x86_64 user adits123 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh logyflag 0 usedti 0 FSGD paireddifftp1tp2.txt labelmask /home/adits123/Desktop/projectoutputdata/fsaverage/label/rh.cortex.label maskinv 0 glmdir rh.paired-diff.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 ResidualFWHM -nan SearchSpace 32101.581527 anattype surface

---

The left hemisphere says pretty much the same thing, with the ResidualFWHM 0.000000 and SearchSpace 44094.721767

Thanks Koushik

---

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: Friday, May 06, 2016 10:46 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim error

The problem is with the estimate of the FWHM for that run. Can you re-run mri_glmfit and send me the command line and terminal output?

On 05/06/2016 10:27 AM, Govindarajan, Koushik Athreya wrote:

...

Dear FS experts,

      I ran into an error with one of my mri_glmfit-sim execution

and was not sure what was going on. The same simulation is currently running for the left hemisphere without any hiccups but I get this following error for the right hemisphere:

---

cd /home/adits123/Desktop/projectoutputdata /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir --sim mc-z 10000 1.3 mc-z.pos.1.3 --sim-sign pos --cwpvalthresh 0.05

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Thu May 5 13:16:51 CDT 2016 Linux localhost.localdomain 2.6.32-250.el6.x86_64 #1 SMP Tue Mar 6 23:00:19 EST 2012 x86_64 x86_64 x86_64 GNU/Linux adits123 setenv SUBJECTS_DIR /home/adits123/Desktop/projectoutputdata FREESURFER_HOME /usr/local/freesurfer

Original mri_glmfit command line: cmdline mri_glmfit --glmdir rh.paired-diff.glmdir --y rh.paired-diff.thickness.sm05.mgh --fsgd paireddifftp1tp2.txt --C contrastpaired.mtx --surf fsaverage rh

DoSim = 1 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = -nan nSimPerJob = 10000 1/1 Thu May 5 13:16:51 CDT 2016 mri_glmfit --y /home/adits123/Desktop/projectoutputdata/rh.paired-diff.thickness.sm05.mgh --C /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/tmp.mri_glmfit-sim-931/contrastpaired.mtx --mask /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/mask.mgh --sim mc-z 10000 1.3 /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001 --sim-sign pos --fwhm -nan --fsgd /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/y.fsgd dods --surf fsaverage rh white simbase /home/adits123/Desktop/projectoutputdata/rh.paired-diff.glmdir/csd/mc-z.pos.1.3.j001 FWHM = -nan ERROR: input FWHM is NaN (not a number). Check the mask in the glm directory. Thu May 5 13:16:51 CDT 2016 ERROR: cannot find any csd files

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I am not sure what the fwhm is NaN error is and also why it is only showing up for one hemisphere. Any help is appreciated.

Thanks Koushik Govindarajan

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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed... www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...

-- 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://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.ed... www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.ed...

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