[Freesurfer] Error viewing uncorrected sign map with freeview
Dear Freesurfer group - I am receiving the following error when I try view results of a mri_glmfit. Any assistance would be greatly appreciated. Thanks, Chaz freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_worstpain_age.glmdir/worstpain/sig.mgh:overlay_threshold=4,5 -viewport 3d Unrecognized sub-option flag 'annot_outline'. FREESURFER_HOME: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.5.0 x86_64 - Please include the following additional information in your report: 1) subject name 2) the entire command-line executed 3) the error message generated 4) optionally include the subject's /script/recon-all.log ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] mri_glmfit fsgd and matrix problems
Hi Freesurfer group - I am receiving errors each time I try to run mri_glmfit. It appears to be the way I set up either the fsgd or mtx file. Any assistance would be greatly appreciated. Thanks, Chaz Hypothesis for the contrast in the mtx file: Is there an average affect of heat threshold regressing out the effect of gender and age? Command-line executed: mri_glmfit \--y lh.heatthreshold.thickness.10.mgh \--fsgd heatthreshold.fsgd dods \--C g1g2.heatthreshold.age.mtx \--surf fsaverage lh \--cortex \--glmdir lh.gender.heatthreshold.age.glmdir I seem to be getting 1 or 2 errors 1: gdfReadHeader: reading heatthreshold1.fsgd INFO: ignoring tag B113v1 INFO: ignoring tag B036V1 INFO: ignoring tag B015v1 INFO: ignoring tag B006v1 WARNING: gdfReadV1: class Male is defined but not used. INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 HeatThreshold nan nan 1 Age nan nan Class Means of each Continuous Variable 1 Male nan nan 2 Female nan nan INFO: gd2mtx_method is dods Reading source surface /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Volumes/projects/painimaging/Bishop/Abstracts/APS_2016/Correlation_Cortical_Thickness_Pain Sensitivity/FSGDs/heat_threshold cmdline mri_glmfit --y lh.heatthreshold.thickness.10.mgh --fsgd heatthreshold1.fsgd dods --C g1g2.heatthreshold.age.mtx --surf fsaverage lh --cortex --glmdir lh.gender.heatthreshold.age.glmdir sysname Darwin hostname phhp-chazgay-mb.ad.ufl.edu machine x86_64 user chaz.gay FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Volumes/projects/painimaging/Bishop/Abstracts/APS_2016/Correlation_Cortical_Thickness_Pain Sensitivity/FSGDs/heat_threshold/lh.heatthreshold.thickness.10.mgh logyflag 0 usedti 0 FSGD heatthreshold1.fsgd labelmask /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.gender.heatthreshold.age.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.gender.heatthreshold.age.glmdir Loading y from /Volumes/projects/painimaging/Bishop/Abstracts/APS_2016/Correlation_Cortical_Thickness_Pain Sensitivity/FSGDs/heat_threshold/lh.heatthreshold.thickness.10.mgh INFO: gd2mtx_method is dods Saving design matrix to lh.gender.heatthreshold.age.glmdir/Xg.dat Normalized matrix condition is 1e+08 Design matrix -- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y lh.heatthreshold.thickness.10.mgh --fsgd heatthreshold1.fsgd dods --C g1g2.heatthreshold.age.mtx --surf fsaverage lh --cortex --glmdir lh.gender.heatthreshold.age.glmdir 2. The FSGD file (if using one) 3. And the design matrix above And 2 gdfReadHeader: reading heatthreshold.fsgd ERROR: gdfReadV1: Input line 1, subjid = B113v1 Found 242 variables, expected. 2 FSGDF Format Error: file = heatthreshold.fsgd, tag=Input I attached both the .mxt and fsgd files Thanks again, Chaz FREESURFER_HOME: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.5.0 x86_64 - Please include the following additional information in your report: 1) subject name 2) the entire command-line executed 3) the error message generated 4) optionally include the subject's /script/recon-all.log heatthreshold.fsgd Description: heatthreshold.fsgd g1g2.heatthreshold.age.mtx Description: g1g2.heatthreshold.age.mtx ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] preproc-sess and stc question
Hi - 1) I am trying to perform preprocessing steps on functional task data that was acquired on a Phillips scanner using an interleaved acquisition. There are 42 slices and the order is [0,6,12,18,24,30,36,1,7,13,19,25,31,37,2,8,14,20,26,32,38,3,9,15,21,27,33,39,4,10,16,22,28,34,40,5,11,17,23,29,35,41]. I've tried -slice order followed by the sequence but that didn't seem to work. And I wasn't able to find anything in stc-sess -help that explained how to enter the exact sequence order. If you could show me how to add/change the tutorial code below, that would be great. Thanks. 2) Do I need to modify the onsets in the paradigmfile? Thanks, Chaz preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] fast_selxavg3 ( ) failed\n
Hi Doug - I've been experimenting with different approaches to link freesurfer with matlab but to no avail. Any assistance would be greatly appreciated. The most recent attempt used the following code. In a fresh terminal window (tsch) I'd set the environment for FREESURFER_HOME and SUBJECTS_DIR and link source with SetUpFreeSurfer.csh. In addition i would set the path to matlab and make it possible to call matlab from the terminal when i type 'matlab' with the code below: alias matlab /Applications/MATLAB_R2014b.app/bin/matlab -nodesktop I'd go to the appropriate folder 'Projects' and rerun the same fast-selxavg3 script. I'd get the same error message, i.e. matlab: command not found again any thoughts on this would be greatly appreciated. Thanks Chaz On Fri, 21 Aug 2015 14:15:05 -0400, Douglas Greve wrote: Do you have matlab installed? If so, is it in your path? On 8/18/15 4:54 PM, Gay,Charles Wysaw wrote: Hi - I've encountered an error in step 8 of the functional connectivity analysis. here is some of the information requested with errors: FREESURFER_HOME: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.0.0 x86_64 - Please include the following additional information in your report: 1) subject name: B113v1 2) the entire command-line executed: selxavg3-sess -s B113v1 -a fc.linsulaseed.surf.lh %step 7 code was: mkanalysis-sess -analysis fc.linsulaseed.surf.lh -surface fsaverage lh -fwhm 5 -notask -taskreg L_Insula.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd rest -TR 2 -per-session %which completed successfully 3) the error message generated :Started at Wed Aug 12 12:56:41 EDT 2015 Ended at Wed Aug 12 13:11:49 EDT 2015 preproc-sess done --- /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1 Wed Aug 12 13:11:50 EDT 2015 anadir = /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/fc.linsulaseed.surf.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 -- --- matlab output matlab: Command not found. -- ERROR: fast_selxavg3() failed\n 4) optionally include the subject's /script/recon-all.log: I included the recon-all.log and selxavg3-sees-rest-fc...log On A previous post I saw the command which matlab was asked: below is the result when I entered it:which matlab matlab: Command not found. Thanks for assistance, chaz ___ 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 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] fast_selxavg3 ( ) failed\n
Hi - I've encountered an error in step 8 of the functional connectivity analysis. here is some of the information requested with errors: FREESURFER_HOME: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.0.0 x86_64 - Please include the following additional information in your report: 1) subject name: B113v1 2) the entire command-line executed: selxavg3-sess -s B113v1 -a fc.linsulaseed.surf.lh %step 7 code was: mkanalysis-sess -analysis fc.linsulaseed.surf.lh -surface fsaverage lh -fwhm 5 -notask -taskreg L_Insula.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd rest -TR 2 -per-session %which completed successfully 3) the error message generated :Started at Wed Aug 12 12:56:41 EDT 2015 Ended at Wed Aug 12 13:11:49 EDT 2015 preproc-sess done --- /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1 Wed Aug 12 13:11:50 EDT 2015 anadir = /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/fc.linsulaseed.surf.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 -- --- matlab output matlab: Command not found. -- ERROR: fast_selxavg3() failed\n 4) optionally include the subject's /script/recon-all.log: I included the recon-all.log and selxavg3-sees-rest-fc...log On A previous post I saw the command which matlab was asked: below is the result when I entered it:which matlab matlab: Command not found. Thanks for assistance, chaz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] fcseed-sess problem
/B113v1/rest/001/tmp.fcseed-sess.55576/seg.nii.gz frame 0 nErode3d 0 nErode2d 0 output /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/mask.nii.gz Binarizing based on matching values nMatch 1 019 binval1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done mri_segstats --i /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/fmcpr.nii.gz --seg /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/mask.nii.gz --id 1 --sum /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/junk.sum --avgwfvol /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/avgwf.mgh $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --i /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/fmcpr.nii.gz --seg /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/mask.nii.gz --id 1 --sum /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/junk.sum --avgwfvol /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/avgwf.mgh sysname Darwin hostname phhp-chazgay-mb.ad.ufl.edu machine x86_64 user chaz.gay UseRobust 0 Loading /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/mask.nii.gz Loading /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/fmcpr.nii.gz Voxel Volume is 27 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0.000 MRIalloc(0, 1, 1): bad parm Reporting on 0 segmentations Computing spatial average of each frame Writing to /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/avgwf.mgh Segmentation fault On Wed, 12 Aug 2015 10:40:14 -0400, Douglas N Greve wrote: Hi Chaz, we'll need more info. Please see surfer.nmr.mgh.harvard.edu/fswiki/BugReporting On 08/11/2015 11:40 PM, Gay,Charles Wysaw wrote: I've completed steps 1 thru 4 successfully (i think). When I run the fcseed-sess with the segid for the left insula I'm getting an segmentation fault. I've tried both segids 7 and 19 and have the same result. Selecting other seed regions (left posterior cingulate) generates a 1d file timecourse. the error log was the same both times: MRIalloc(0, 1, 1): bad parm Any ideas on what to do? Thanks Chaz ___ 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 gr...@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 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. recon-all-status.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] fcseed-sess problem
Thank you. issue resolved. On Wed, 12 Aug 2015 11:20:53 -0400, Douglas N Greve wrote: The problem is that you are using the wrong segmentation number for left insula. You used 19, which is reasonable given that FreeSurferColorLUT.txt lists that as left insula, but the one you want is actually 1035. doug On 08/12/2015 11:09 AM, Gay,Charles Wysaw wrote: Hi Doug - Here is some of the information: FREESURFER_HOME: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.0.0 x86_64 - Please include the following additional information in your report: 1) subject name: B113v1 2) the entire command-line executed: [phhp-chazgay-mb:Bishop/FreeSurfer_R01/Project] chaz.gay% fcseed-sess -s B113v1 -cfg mean.L_Insula.config 3) the error message generated: see below - 4) optionally include the subject's /script/recon-all.log: attached. 5) SUBJECTS_DIR: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects Logfile is /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/log/fcseed-sess.L_Insula.dat.log.B113v1 Wed Aug 12 11:03:33 EDT 2015 Darwin phhp-chazgay-mb.ad.ufl.edu 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 setenv SUBJECTS_DIR /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects cd /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/fsfast/bin/fcseed-sess -s B113v1 -cfg mean.L_Insula.config freesurfer-Darwin-lion-stable-pub-v5.3.0 Wed Aug 12 11:03:33 EDT 2015 Darwin phhp-chazgay-mb.ad.ufl.edu 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 setenv SUBJECTS_DIR /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects cd /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/fsfast/bin/fcseed-sess -s B113v1 -cfg mean.L_Insula.config freesurfer-Darwin-lion-stable-pub-v5.3.0 mri_label2vol --seg /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects/B113v1/mri/aparc+aseg.mgz --reg /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/register.dof6.dat --temp /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/template.nii.gz --fillthresh .5 --o /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/seg.nii.gz --pvf /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/pvf.nii.gz PVF /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/pvf.nii.gz Number of labels: 0 Annot File: (null) Template Volume: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/template.nii.gz Outut Volume: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/seg.nii.gz Registration File: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/register.dof6.dat Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ Template RAS-to-Vox: -0.333 0.000 0.000 40.000; -0.000 -0.000 -0.333 40.000; -0.000 0.333 -0.000 19.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 27 nHits Thresh: 13.5 Loading registration from /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/register.dof6.dat RegMat: 1.000 -0.011 -0.001 9.758; -0.002 -0.246 0.969 -27.653; 0.011 0.969 0.246 -1.912; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -0.333 0.004 0.000 36.747; -0.004 -0.323 -0.082 40.637; -0.001 -0.082 0.323 9.782; 0.000 0.000 0.000 1.000; ASeg2Vol: Building LUT ASeg2Vol: Sorting ASeg2Vol: Mapping ASeg2Vol: Reverse Map nmisses = 234 (0 filled) ASeg2Vol: done PVF /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/pvf.nii.gz Computing PVF 27 mri_binarize --i /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/seg.nii.gz --o /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/mask.nii.gz --match 19 $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp
[Freesurfer] fcseed-sess problem
I've completed steps 1 thru 4 successfully (i think). When I run the fcseed-sess with the segid for the left insula I'm getting an segmentation fault. I've tried both segids 7 and 19 and have the same result. Selecting other seed regions (left posterior cingulate) generates a 1d file timecourse. the error log was the same both times: MRIalloc(0, 1, 1): bad parm Any ideas on what to do? Thanks Chaz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
