Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

1.5T GE dicom images into FreeSurfer
by pdavis＠westol.com 20 Feb '16

20 Feb '16

Hi, We would like to process 1.5 T GE dicom scans for over 200 individuals. It is unclear how to import these into FreeSurfer and process in batch. Each subject folder consists of several subfolders. Each subfolder consists of all the images of a single pulse sequence, e.g. sagittal spgr, axial T2, etc. The images in the subfolders are files labeled I.001.dcm, I.002.dcm, ... . Each image is a valid dicom image which can be individually opened in other dicom viewing programs. However, the entire series of images in the subfolder is not automatically recognized as a 3D set. Thank you, Peter Davis -------------------------------------------------------------------- mail2web.com ? What can On Demand Business Solutions do for you? http://link.mail2web.com/Business/SharePoint

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Error in surface-based interhemispheric registration
by Ilaria Mazzonetto 20 Feb '16

20 Feb '16

Hi Freesurfer experts, I'm using freesurfer v5.2.0. If I use surfreg --s $subject --t fsaverage_sym --lh, I have this error: ERROR: cannot find /home/T1/fsaverage_sym/lh.reg.template.tif. Does anyone know how can I fix this? Thanks a lot. Ilaria

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Fwd: Job Offer in Madrid
by José Ángel Pineda 20 Feb '16

20 Feb '16

We are pleased to offer a 2-year post-doctoral position at the Reina Sofia Foundation Alzheimer's Disease Centre in Madrid, Spain. The successful applicant will be involved in neuroimaging analyses of a 5-year longitudinal study (currently in year 4) of 1200 healthy elderly individuals (aged 70-85) to determine neuronal markers in the healthy state which predict subsequent development of mild cognitive impairment and dementia. In addition, the Reina Sofia Alzheimer's Centre offers: - A research-dedicated MRI facility attached to a 140-bed residence for patients with Alzheimer’s disease. - A brain-bank providing post-mortem histopathological confirmation of dementia diagnosis for patients scanned pre-mortem. - Ex-vivo MRI scanning. A strong background in neuroimaging techniques is required. Applicants must have a PhD in neuroscience, cognitive neuroscience, biomedical engineering, neuropsychology or related field. Experience in dementia research is a plus. Spanish language skills are NOT required. Competitive annual salary depending on experience. SUBMISSION Interested candidates should send CV and a cover letter (including contact details of 2 referees), to the following email address: bryan.strange(a)upm.es DEADLINE FOR SUBMISSION OF APPLICATIONS March 4, 2016 Any questions, please feel free to contact me.

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Re: [Freesurfer] Building from source -- autoconf error
by Z K 20 Feb '16

20 Feb '16

Hello Yaroslav, Ive built freesurfer on Debian "Jessie" platform. It was just a matter of adding "libtool-bin" and "tcsh" to the list of packages that need to be installed. Ive update the wiki page: https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page I still wasnt quite able to get the freeview GUI to build. But If you change the "--disable-GUI-build" flag to "--without-qt" then you will get all the tktool GUIs except freeview. Im working on getting freeview to build at the moment and will update the wiki page once I figure it out. -Zeke On 02/18/2016 05:04 PM, Yaroslav Halchenko wrote: > Gotcha, thanks! > > On February 18, 2016 3:27:21 PM EST, Z K <zkaufman(a)nmr.mgh.harvard.edu> wrote: >> >>> I would be infinitely grateful if freesurfer could build natively on >> Debian >>> stable! ;) Thanks for trying. In my case I am trying the build >> under jessie >>> chroot (using schroot helper), so I could quickly setup/enter such >> environment >>> while maintaining user/directory. I will do the same now for 14.04. >> If you >>> would like more -- let me know I could give a bit more detailed >>> instructions. >>> >> >> I have a debian jessie system just setup, but I have a high priority >> project due Monday, so I would be able to begin determining the exact >> build procedure on Debian jessie until beginning of next week. It is >> something I have been meaning to do so I plan on getting to it. If you >> dont hear from me by Tuesday/Wedensday feel free to shoot me an email >> for an update. Thanks. >> >> -Zeke >> >> >> 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. >

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R: Re: R: FS-FAST using MRS voxel or .label as seed
by stdp82＠virgilio.it 19 Feb '16

19 Feb '16

By running mri_cor2label --i $SUBJECTS_DIR/mri/MRS_MASK.nii.gz --id 1 --l MRS.label and opening the MRS.label by tksurfer fsaverage rh inflate -aparc -overlay MRS. label the inflate is empty. Stefano >----Messaggio originale---- >Da: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >Data: 19-feb-2016 0.34 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: FS-FAST using MRS voxel or .label as seed > >That is an incorrect usage of mri_cor2label. MRS_MASK.nii.gz is a >volume, not a surface overlay. By using --surf, you are indicating that >it is a surface overlay > >On 02/18/2016 06:30 PM, stdp82(a)virgilio.it wrote: >> Furthermore, if I use mir_cor2label in order to show the location of >> MRS voxel (in native space) this error occurs: >> >> mri_cor2label --c $SUBJECTS_DIR/subj/MRS_MASK.nii.gz --id 1 --l >> MRS.label --surf fsaverage lh >> $Id: mri_cor2label.c,v 1.12 2011/03/02 00:04:14 nicks Exp $ >> Loading mri >> /Applications/freesurfer/subjects/subject_dir/subj/MRS_MASK.nii.gz >> Loading >> /Applications/freesurfer/subjects/subject_dir/fsaverage/surf/lh.white >> ERROR: dim mismatch between surface (163842) and input (16777216) >> >> ----Messaggio originale---- >> Da: stdp82(a)virgilio.it >> Data: 19-feb-2016 0.10 >> A: <freesurfer(a)nmr.mgh.harvard.edu> >> Ogg: [Freesurfer] FS-FAST using MRS voxel or .label as seed >> >> Hi list, >> >> I'm having problem to use FS-FAST fMRI connectivity using as seed >> a mask of a MRS voxel or .label obtained by drawing it from >> surface. In order to resolve my concern, I'm reporting step by >> step the command lines which I have used. The mask, f.nii.gz, >> orig.nii.gz and aparc+aseg.nii.gz showed a good overlap. >> >> These are the features of each one: >> >> fslinfo orig.nii.gz >> >> data_type UINT8 >> >> dim1 256 >> >> dim2 256 >> >> dim3 256 >> >> dim4 1 >> >> datatype 2 >> >> pixdim1 1.000000 >> >> pixdim2 1.000000 >> >> pixdim3 1.000000 >> >> pixdim4 0.010747 >> >> cal_max 0.0000 >> >> cal_min 0.0000 >> >> file_type NIFTI-1+ >> >> fslinfo aparc+aseg.nii.gz >> >> data_type INT32 >> >> dim1 256 >> >> dim2 256 >> >> dim3 256 >> >> dim4 1 >> >> datatype 8 >> >> pixdim1 1.000000 >> >> pixdim2 1.000000 >> >> pixdim3 1.000000 >> >> pixdim4 0.010747 >> >> cal_max 0.0000 >> >> cal_min 0.0000 >> >> file_type NIFTI-1+ >> >> fslinfo MRS_MASK.nii.gz >> >> data_type FLOAT32 >> >> dim1 256 >> >> dim2 256 >> >> dim3 256 >> >> dim4 1 >> >> datatype 16 >> >> pixdim1 1.000000 >> >> pixdim2 1.000000 >> >> pixdim3 1.000000 >> >> pixdim4 0.000000 >> >> cal_max 0.0000 >> >> cal_min 0.0000 >> >> file_type NIFTI-1+ >> >> I’m using MNI2mm for subcortical analysis. >> >> mri_convert $SUBJECTS_DIR/Subj/MRS_Voxel_FS_space.nii.gz >> $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz >> >> fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz >> -fsd rest -mean -cfg MRS_MASK.config –overwrite >> >> fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite >> >> mkanalysis-sess -analysis fc.MRS_MASK.surf.lh -surface fsaverage >> lh -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 >> -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 >> -per-run -overwrite >> >> mkanalysis-sess -analysis fc.MRS_MASK.surf.rh -surface fsaverage >> rh -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 >> -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 >> -per-run -overwrite >> >> mkanalysis-sess -analysis fc.MRS_MASK.mni305 -mni305 -fwhm 8 >> -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 >> -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run -overwrite >> >> selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.rh >> >> selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.lh >> >> selxavg3-sess -sf sessid -a fc.MRS_MASK.mni305 >> >> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.rh -contrast >> MRS_MASK -o my-group >> >> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.lh -contrast >> MRS_MASK -o my-group >> >> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.mni305 -contrast >> MRS_MASK -o my-group >> >> When I run fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite, >> it seem to be functioning for the first subj, but the next subj2 >> show this error >> >> Loading >> /Applications/freesurfer/subjects/fMRI/subj2/rest/001/fmcpr.nii.gz >> >> Voxel Volume is 64.5752 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 >> //Applications/freesurfer/subjects/fMRI/subj2/rest/001/tmp.fcseed-sess. 28328/avgwf.mgh >> >> Segmentation fault >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)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(a)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. > >

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R: Re: FS-FAST using MRS voxel or .label as seed
by stdp82＠virgilio.it 19 Feb '16

19 Feb '16

The problem persist. Stefano >----Messaggio originale---- >Da: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >Data: 19-feb-2016 0.25 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] FS-FAST using MRS voxel or .label as seed > > >I think it may be our fcseed-config command line >fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz -fsd >rest -mean -cfg MRS_MASK.config –overwrite > >It should be -seg MRS_MASK.mgz > >They way you have it, fcseed will use the segmentation for Subj for all >subjects, which is why it works for one and not for others > > >On 02/18/2016 06:10 PM, stdp82(a)virgilio.it wrote: >> >> Hi list, >> >> I'm having problem to use FS-FAST fMRI connectivity using as seed a >> mask of a MRS voxel or .label obtained by drawing it from surface. In >> order to resolve my concern, I'm reporting step by step the command >> lines which I have used. The mask, f.nii.gz, orig.nii.gz and >> aparc+aseg.nii.gz showed a good overlap. >> >> These are the features of each one: >> >> fslinfo orig.nii.gz >> >> data_type UINT8 >> >> dim1 256 >> >> dim2 256 >> >> dim3 256 >> >> dim4 1 >> >> datatype 2 >> >> pixdim1 1.000000 >> >> pixdim2 1.000000 >> >> pixdim3 1.000000 >> >> pixdim4 0.010747 >> >> cal_max 0.0000 >> >> cal_min 0.0000 >> >> file_type NIFTI-1+ >> >> fslinfo aparc+aseg.nii.gz >> >> data_type INT32 >> >> dim1 256 >> >> dim2 256 >> >> dim3 256 >> >> dim4 1 >> >> datatype 8 >> >> pixdim1 1.000000 >> >> pixdim2 1.000000 >> >> pixdim3 1.000000 >> >> pixdim4 0.010747 >> >> cal_max 0.0000 >> >> cal_min 0.0000 >> >> file_type NIFTI-1+ >> >> fslinfo MRS_MASK.nii.gz >> >> data_type FLOAT32 >> >> dim1 256 >> >> dim2 256 >> >> dim3 256 >> >> dim4 1 >> >> datatype 16 >> >> pixdim1 1.000000 >> >> pixdim2 1.000000 >> >> pixdim3 1.000000 >> >> pixdim4 0.000000 >> >> cal_max 0.0000 >> >> cal_min 0.0000 >> >> file_type NIFTI-1+ >> >> I’m using MNI2mm for subcortical analysis. >> >> mri_convert $SUBJECTS_DIR/Subj/MRS_Voxel_FS_space.nii.gz >> $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz >> >> fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz -fsd >> rest -mean -cfg MRS_MASK.config –overwrite >> >> fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite >> >> mkanalysis-sess -analysis fc.MRS_MASK.surf.lh -surface fsaverage lh >> -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg >> wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run >> -overwrite >> >> mkanalysis-sess -analysis fc.MRS_MASK.surf.rh -surface fsaverage rh >> -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg >> wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run >> -overwrite >> >> mkanalysis-sess -analysis fc.MRS_MASK.mni305 -mni305 -fwhm 8 -notask >> -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 >> -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run -overwrite >> >> selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.rh >> >> selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.lh >> >> selxavg3-sess -sf sessid -a fc.MRS_MASK.mni305 >> >> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.rh -contrast >> MRS_MASK -o my-group >> >> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.lh -contrast >> MRS_MASK -o my-group >> >> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.mni305 -contrast >> MRS_MASK -o my-group >> >> When I run fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite, >> it seem to be functioning for the first subj, but the next subj2 show >> this error >> >> Loading /Applications/freesurfer/subjects/fMRI/subj2/rest/001/fmcpr.nii.gz >> >> Voxel Volume is 64.5752 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 >> //Applications/freesurfer/subjects/fMRI/subj2/rest/001/tmp.fcseed-sess. 28328/avgwf.mgh >> >> Segmentation fault >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)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(a)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. > >

2 1

Paired t-test for correlation analysis on two time points
by amirhossein manzouri 19 Feb '16

19 Feb '16

Hi, We would like to run paired t-test on longitudinal within group data for correlation analysis of one measurement and cortical thickness, not cortical thickness comparison at the respective time point . I found the paired analysis and read that but in fact we need to see if correlation between our measure and CTH differs from time point one to time point 2. So the question will does the thickness and measure1 correlation differs between time point1 and tp2? Best regards, Amirhossein Manzouri

3 9

comparison between two hemisphere in single
by Ashkan Faghiri 19 Feb '16

19 Feb '16

Hello, sorry for asking this again I want to calculate the difference between the thickness of one subjects different hemispheres and show this on pial (left or right or even fsaverage_sys). so I have ran : surfreg --s $subject --t fsaverage_sym --lh surfreg --s $subject --t fsaverage_sym --lh --xhemi for my one subject. now I have two .reg files: shahi/xhemi/surf/lh.fsaverage_sym.sphere.reg shahi/surf/lh.fsaverage_sym.sphere.reg If I am understanding this right, these two are the transform matrix for both hemisphere of my one subject to fsaverage_sym (*right?*) if I run mris_preproc with xhemi option I will get a vector which have the length equal to number of vertexes. it's values are left-right (*or right-left?*). how can I convert this vector to pial or inflated surface? and how can I use lh.fsaverage_sym.sphere.reg to register my pial directly to fsaverage_sym? Regards, Ashkan -- -- Ashkan Faghiri MSc student of Bioelectrical Engineering Department of Electrical Engineering Sharif University of Technology

2 1

Centos7 and OpenSuse Leap42 License
by Malina, Thomas (EKA) 19 Feb '16

19 Feb '16

Hello, I have problems with the license if try to run freesurfer under OpenSuse Lap 42. I alway get the message ERROR: Invalid FreeSurfer license key found in license file. What can I do? I have installed CENT OS7 just for testing, but I´m not very familiar with this os. The funny situation there is, that I can put anything in the license.txt even empty file and the programms will start without errors. You can see it on the screenshots attached. I don´t have any .license file in the freesurfer directory. Greetings, Thomas Malina Vertraulichkeitsvermerk: Der Inhalt dieser E-Mail ist vertraulich und unterliegt möglicherweise dem Datenschutz. Wenn Sie diese E-Mail irrtümlich erhalten haben, löschen Sie sie bitte und benachrichtigen Sie bitte umgehend telefonisch oder per E-Mail den Absender. Diese E-Mail darf weder kopiert oder für andere Zwecke verwendet werden noch darf ihr Inhalt anderen Personen offen gelegt werden.

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R: Re: FS-FAST using MRS voxel or .label as seed
by stdp82＠virgilio.it 19 Feb '16

19 Feb '16

I have also run as followed but the error persist. mri_convert $SUBJECTS_DIR/Subj2/MRS_Voxel_FS_space.nii.gz $SUBJECTS_DIR/Subj2/mri/MRS_MASK2.mgz mri_convert $SUBJECTS_DIR/Subj2/MRS_Voxel_FS_space.nii.gz MRS_MASK2.mgz fcseed-config -segid 1 -seg MRS_MASK2.mgz -fsd rest -mean -cfg MRS_MASK2. config -overwrite fcseed-sess -s Subj2 -cfg MRS_MASK2.config -overwrite >----Messaggio originale---- >Da: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >Data: 19-feb-2016 0.25 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] FS-FAST using MRS voxel or .label as seed > > >I think it may be our fcseed-config command line >fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz -fsd >rest -mean -cfg MRS_MASK.config –overwrite > >It should be -seg MRS_MASK.mgz > >They way you have it, fcseed will use the segmentation for Subj for all >subjects, which is why it works for one and not for others > > >On 02/18/2016 06:10 PM, stdp82(a)virgilio.it wrote: >> >> Hi list, >> >> I'm having problem to use FS-FAST fMRI connectivity using as seed a >> mask of a MRS voxel or .label obtained by drawing it from surface. In >> order to resolve my concern, I'm reporting step by step the command >> lines which I have used. The mask, f.nii.gz, orig.nii.gz and >> aparc+aseg.nii.gz showed a good overlap. >> >> These are the features of each one: >> >> fslinfo orig.nii.gz >> >> data_type UINT8 >> >> dim1 256 >> >> dim2 256 >> >> dim3 256 >> >> dim4 1 >> >> datatype 2 >> >> pixdim1 1.000000 >> >> pixdim2 1.000000 >> >> pixdim3 1.000000 >> >> pixdim4 0.010747 >> >> cal_max 0.0000 >> >> cal_min 0.0000 >> >> file_type NIFTI-1+ >> >> fslinfo aparc+aseg.nii.gz >> >> data_type INT32 >> >> dim1 256 >> >> dim2 256 >> >> dim3 256 >> >> dim4 1 >> >> datatype 8 >> >> pixdim1 1.000000 >> >> pixdim2 1.000000 >> >> pixdim3 1.000000 >> >> pixdim4 0.010747 >> >> cal_max 0.0000 >> >> cal_min 0.0000 >> >> file_type NIFTI-1+ >> >> fslinfo MRS_MASK.nii.gz >> >> data_type FLOAT32 >> >> dim1 256 >> >> dim2 256 >> >> dim3 256 >> >> dim4 1 >> >> datatype 16 >> >> pixdim1 1.000000 >> >> pixdim2 1.000000 >> >> pixdim3 1.000000 >> >> pixdim4 0.000000 >> >> cal_max 0.0000 >> >> cal_min 0.0000 >> >> file_type NIFTI-1+ >> >> I’m using MNI2mm for subcortical analysis. >> >> mri_convert $SUBJECTS_DIR/Subj/MRS_Voxel_FS_space.nii.gz >> $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz >> >> fcseed-config -segid 1 -seg $SUBJECTS_DIR/Subj/mri/MRS_MASK.mgz -fsd >> rest -mean -cfg MRS_MASK.config –overwrite >> >> fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite >> >> mkanalysis-sess -analysis fc.MRS_MASK.surf.lh -surface fsaverage lh >> -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg >> wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run >> -overwrite >> >> mkanalysis-sess -analysis fc.MRS_MASK.surf.rh -surface fsaverage rh >> -fwhm 8 -notask -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg >> wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run >> -overwrite >> >> mkanalysis-sess -analysis fc.MRS_MASK.mni305 -mni305 -fwhm 8 -notask >> -taskreg MRS_MASK 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 >> -nskip 4 -mcextreg -fsd rest -TR 1.1 -per-run -overwrite >> >> selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.rh >> >> selxavg3-sess -sf sessid -a fc.MRS_MASK.surf.lh >> >> selxavg3-sess -sf sessid -a fc.MRS_MASK.mni305 >> >> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.rh -contrast >> MRS_MASK -o my-group >> >> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.surf.lh -contrast >> MRS_MASK -o my-group >> >> isxconcat-sess -sf sessid -analysis fc.MRS_MASK.mni305 -contrast >> MRS_MASK -o my-group >> >> When I run fcseed-sess -s Subj -cfg MRS_MASK.config -overwrite, >> it seem to be functioning for the first subj, but the next subj2 show >> this error >> >> Loading /Applications/freesurfer/subjects/fMRI/subj2/rest/001/fmcpr.nii.gz >> >> Voxel Volume is 64.5752 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 >> //Applications/freesurfer/subjects/fMRI/subj2/rest/001/tmp.fcseed-sess. 28328/avgwf.mgh >> >> Segmentation fault >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)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(a)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. > >

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