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16 participants
30098 discussions

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.

1 0

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. > >

1 0

Entorhinal thickness
by Mohamed Ali Bahri 19 Feb '16

19 Feb '16

Dear Freesurfer, The entorhinal has different volume and thickness in the "?h_aparc.stats" & "?h.entorhinal_exvivo.stats" files. Could any one explain way and which one should be used? Many thanks in advance, Best regards, Mohamed -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Cyclotron Research Centre, University of Liège, Belgium m.bahri(a)ulg.ac.be

3 3

R: FS-FAST using MRS voxel or .label as seed
by stdp82＠virgilio.it 18 Feb '16

18 Feb '16

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.gzLoading /Applications/freesurfer/subjects/subject_dir/fsaverage/surf/lh.whiteERROR: 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 96 Normal 0 14 false false false IT X-NONE X-NONE table.MsoNormalTable {mso-style-name:"Tabella normale"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:Calibri; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin;} 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

2 1

FS-FAST using MRS voxel or .label as seed
by stdp82＠virgilio.it 18 Feb '16

18 Feb '16

96 Normal 0 14 false false false IT X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabella normale"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:Calibri; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin;} 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

2 1

I: I: R: R: R: Re: To use a ROI.label as seed in FS-FAST
by stdp82＠virgilio.it 18 Feb '16

18 Feb '16

2 1

Statistical analyses with QDEC
by Francesco Cardinale 18 Feb '16

18 Feb '16

Dear Freesurfer experts, I have some questions about statistical analyses. How to adjust for sex and age? I use the precompiled Freesurfer 5.3.0 MacOSX version, and its tool QDEC to compare cortical thickness between two groups. I would like to use age and sex as nuisance factors. No problem with the age, but I don’t see the sex in the list of usable variables if I code it as a categorical variable (male / female). On the opposite, If I code it as numbers (male = 1, female = 2) I can use it, but how can I declare that it is a factor and not a continuous numerical variable? I don’t want that “female” affects the fitting of the GLM with a value that means “male” * 2. What about the use of other morphometric properties as nuisance factors? For example, how could I use sulcality or LGI as nuisance factors? Is it possible to use more than one scalar simultaneously? Similarly to question 2, is it possible to use home-made *.mgh scalars as a nuisance factors? How? Do the command-line tools allow such analyses better than QDEC? Related to my questions, which features do they add? In this field of interest, are there any major advantages coming with Freesurfer 6.0? Thanks a lot and best regards Cico

2 1

mris_diff documentation
by Suchandra Thapa 18 Feb '16

18 Feb '16

Hi, I'm trying to use the mris_diff command to do some comparisons however I'm having trouble finding documentation aside from the help text that the command outputs. Is there a wiki page that documents the command or some other place with documentation? Suchandra Suchandra Thapa sthapa(a)ci.uchicago.edu Computation Institute Searle Chemistry Laboratory #201A 5735 South Ellis Avenue Chicago, IL 60637

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