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30084 discussions

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

2 1

Fwd: 3D viewing ROIs by Freeview
by Faeze Vedaei 18 Feb '16

18 Feb '16

Hello Freesurfer experts, I am Faezeh Vedaei a research assistant in a neurology lab at the Michigan State University. In my project I want to have a 3D view of ROIs which I just extracted by AFNI, after I executed recon-all. I would like to help me how can I overlay some specific ROIs on a 3D brain map in Freeview? In advance, I would appreciate your time and consideration. Regards, Faezeh Vedaei

3 3

stable6
by Grafe,Brendan P. (BIDMC - Neurology) 18 Feb '16

18 Feb '16

Hello all, I have been slowly processing a longitudinal dataset off and on again since last August, sourcing /usr/local/freesurfer/nmr-stable6-env. Does this represent v.6.0-beta or v.6.0 in development? We were initially interested in applying the hippocampal subfield segmentation functionality on (1mm) T1 MPRAGE acquisitions and have found varying reproducibility, and questionable segmentation, of certain scans. I was aware that these volumetric measurements were to be interpreted with caution, but I'm separately wondering if the data I have processed in this environment can be trusted in analysis of cortical thickness change or if reprocessing with a previous version would be advised. -Brendan ----------------------------- Brendan P. Grafe MSc Clinical Research Assistant Berenson-Allen Center for Noninvasive Brain Stimulation Beth Israel Deaconess Medical Center 330 Brookline Avenue Boston, MA 02215 Tel: 617-667-0256 Fax: 617-975-5322 ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 1

pial edits in subject with severe atrophy
by Corinna Bauer 18 Feb '16

18 Feb '16

Dear Experts, I have a subject with severe atrophy in bilateral frontal and parietal regions and after many rounds of edits to the brainmask, wm.mgz, and control points, these regions are still left uncaptured. Is there a way to edit the pial surface to include these grey matter regions? I am hesitant to draw them in via the wm surface since there is no definite WM present. I do have a FLAIR also on this subject. I've attached a couple examples. Thanks! Corinna

2 6

Help - Surface extraction to Matlab
by Ittai Shamir 18 Feb '16

18 Feb '16

Hello, My name is Ittai and I am currently working on my M.Sc. in the department of Neurobiology in Tel Aviv University. I am a new FreeSurfer user. My question regarding the software is- After successfully running my data (T1 image - MPRAGE) through FS, I would like to extract both cortical surfaces (adjacent to pia and white matter) to Matlab. Is there a simple method of extracting these surface data to Matlab? or converting them to a format that is compatible with Matlab? I would greatly appreciate any help in this matter. Thanks in advance, Ittai Shamir

2 1

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