[Freesurfer] error when running permutation analysis
External Email - Use Caution Dear FS experts, Hi! I ran the commas “mir_glmfit-sim” to do clusterwise correction for permutation but received an error.My command is:mri_glmfit-sim --glmdir rh_thickness_fwhm10 --perm 1000 3 pos --cwp 0.05 --2spaces And I received the following message (The whole log file is attached in the email)Starting simulation sim over 1000 trialsmri_glmfit simulation done 21.2316Mon Jun 7 16:34:28 CST 2021mri_surfcluster --in rh_twoT_thickness_fwhm10/group.diff/sig.mgh --mask rh_twoT_thickness_fwhm10/mask.mgh --cwsig rh_twoT_thickness_fwhm10/group.diff/perm.th30.pos.sig.cluster.mgh --sum rh_twoT_thickness_fwhm10/group.diff/perm.th30.pos.sig.cluster.summary --ocn rh_twoT_thickness_fwhm10/group.diff/perm.th30.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o rh_twoT_thickness_fwhm10/group.diff/perm.th30.pos.sig.masked.mgh --no-fixmni --csd rh_twoT_thickness_fwhm10/csd/perm.th30.pos.j001-group.diff.csd --csdpdf rh_twoT_thickness_fwhm10/group.diff/perm.th30.pos.pdf.dat --vwsig rh_twoT_thickness_fwhm10/group.diff/perm.th30.pos.sig.voxel.mgh --vwsigmax rh_twoT_thickness_fwhm10/group.diff/perm.th30.pos.sig.voxel.max.dat --oannot rh_twoT_thickness_fwhm10/group.diff/perm.th30.pos.sig.ocn.annot --bonferroni 2 --surf white/Applications/freesurfer/bin/mri_surfcluster: Exec format error. Binary file not executable. Then I used “ls -l /Applications/freesurfer/bin/mri_surfcluster” to debug and it returned:-rwx--@ 1 star staff 3626968 9 7 2018 /Applications/freesurfer/bin/mri_surfclusterI wonder what’s wrong with the command I use. ANY ADVISE would be appreciated!THANKS A LOT!Sida Xi, M.D.Department of OphthalmologyEye and ENT Hospital, Fudan University School of Medicine, 83th Fenyang Rd, Xuhui District, Shanghai, China perm.th30.pos.mri_glmfit-sim.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] extract % signal change in FSFAST analysis
External Email - Use Caution Hi, dear FS experts, I'm trying to use mir_segstats to extract % signal change in task fMRI analysis. The command is:mri_segstats --I ./ces.nii.gz --annot fsaverage rh perm.th30.pos.sig.ocn.annot --excludeid 0 --avgwf rh.ces.avgwf.dat;There are two kinds of contract files (ces.nii.gz and cesspit.nii.gz), and I wonder which one should be used to calculate extract % signal change.In another words, if I use “mri_segstats —i cespct.nii.gz --avgwf file.dat”, does the file.dat contain "% signal change" data? (The webpage says “ avewf means computes the average waveform across all the voxel" ) Thx a lot! Star Sida Xi, M.D.Department of OphthalmologyEye and ENT Hospital, Fudan University School of Medicine, 83th Fenyang Rd, Xuhui District, Shanghai, China ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Convert cespct.nii to subject's own anatomy space (for ROI analysis)
External Email - Use Caution Hi FS experts,I’m processing the task related fMRI data and want to extract the 100 most strongly activated voxels with in each of the visual areas (like V1-V3, V3A, MT etc.). It seems to I need to do the ROI analysis using matlab.I meet some problems when convert files from surface space to volume space.Here’s my procedures:1. For each individual, convert cespct.nii to volume space (individual space)mri_vol2vol —mov ces.nii.gz --reg sub/bold/register.lta --fstarg --interp nearest --o cespct.anat.nii (dimension 256*256*256)However, when I use MRIread to import the file, I find the values in cespct.anat.nii are all 0. 2. convert label to volume space (individual space)I want to convert label to the individual space (mri_label2label --outmask) and then convert it to volume space (mri_vol2vol). mri_label2label --srclabel lh.V3A.label --srcsubject fsaverage --trglabel lh.v3a.sub.label --trgsubject sub --regmethod surface --hemi lh --outmask lh.v3a.sub.niimri_info lh.v3a.sub.nii (dimension is 144775x1x1, not 163842x1x1)I’m wondering how can I have a mask in subject’s anatomy space using a label ?Is there anything wrong during the transformation?Any suggestions will be appreciated !THANK YOU!Star ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Difference bewteen beta and ces in FS-FAST
External Email - Use Caution Dear FS experts, Hi!I have a very basic question about GLM model in FS-FAST.After GLM analysis, there is a beta.nii under the analysis/ directory and a ces.nii under each contrast/ directory. In the tutorial, beta.nii is the regression coefficients and ces.nii is contrast effect size (contrast matrix * regression coef). My question is :1. both of them are regression coefficients, what’s the difference bewteen beta.nii and ces.nii.？2. I want to do ROI analysis and extract the signal change in the given ROI from each individual. Which value represent the signal change (beta, ces, ceavar or t)? Any suggestions are welcome!ThanksStarFudan University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ROI Analysis in a given label with Functional Constraint in FSFAST
External Email - Use Caution Thank you for your response. I have 2 questions.1. I want to extract a binary ROI after group analysis with the command:mri_binarize --i lh.sig.nii.gz --min 9.13 --mask lh.V3A.nii.gz --o lh.ROI.nii.gzfreeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.ROI.nii.gz When I overlayed lh.sig.V3A.nii.gz with freeview, I found the edge of the ROI are decimals and voxel inside the mask is 1. I also tried “mri_binarize --zero-edge” but it didn’t work. My question is : how to make a binary ROI (all the voxels below 9.13 is zero). The output file is attached in the email.2. I try to convert the binary ROI in fsaverage space into individual space and extract the average HRF contrast in the ROI in each subject. Here’s my command.# resample the ces.nii.gz volume into the individual’s space mri_vol2vol --mov subj1/ces.nii.gz --reg register.lta --fstarg --interp nearest --o subj1/lh.ces.anat.bb.mgh# resample the ROI volume into the individual’s space mri_surf2surf --hemi lh --srcsubject fsaverage --trgsubject subj1 --reg subj1/register.lta --sval stats/lh.ROI.nii.gz --tval stats/lh.ROI.anat.bb.mgz --hemi lh# extract the average HRF contrast in the ROI from each subjectmri_segstats --i lh.ces.anat.bb.mgh --sum ces.masked.bb.stats --mask lh.sig.V3A.anat.bb.mgzThis step goes wrong with caution “ERROR: must specify a segmentation volume”My question is : how to extract the average HRF contrast in the ROI from each subject ? Is there some option like "--m cespct” in funcroi-table-sess to extract average signal change?ThanksStar Xi On 02/14/2020 23:14，Douglas N. Greve wrote： Is the hV5+MT label already a binary volume in the FS conformed 1mm space (ie, same space as orig.mgz)? And what do you mean by "constrained"? On 2/13/2020 11:04 AM, Star Xi wrote: External Email - Use Caution FS experts, Commonly, I can use mri_vol2vol -> mri_segstats to extract anatomical ROI from aparc or aseg template. However, now I want to extract the average percent signal change in the hV5+/MT by constrained positive functional activation. The anatomical label is from other template. My question is, after using mri_vol2vol, which command can extract signals from a given label with constrained activation ? Thanks, Star ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer lh.ROI.nii.gz Description: GNU Zip compressed data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] ROI Analysis in a given label with Functional Constraint in FSFAST
External Email - Use Caution FS experts,Commonly, I can use mri_vol2vol -> mri_segstats to extract anatomical ROI from aparc or aseg template.However, now I want to extract the average percent signal change in the hV5+/MT by constrained positive functional activation. The anatomical label is from other template.My question is, after using mri_vol2vol, which command can extract signals from a given label with constrained activation ?Thanks,Star ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FSFAST registration
External Email - Use Caution Dear FS experts, I’m processing the task-related fMRI using FS-FAST. I check the quality assurance and modified some subjects’ registration file(named new one as “register_manual.lta”). Then I do the first level analysis and group analysis. My first question is: should I apply the new registration file into the following first level analysis and group analysis? I found a tutorial may be answer my question , but I’m not sure about it. http://surfer.nmr.mgh.harvard.edu/fswiki/MultiModalTutorialV6.0/FMRIGroupAnalysis#GroupROIfMRIAnalysis Assemble the data using new registration file by the command: mris_preproc --target fsaverage --hemi lh \ --iv fbirn-101/ces.nii fbirn-101/register.lta \ --iv fbirn-103/ces.nii fbirn-103/register.lta \ --iv fbirn-104/ces.nii fbirn-104/register.lta \ --projfrac 0.5 \ --out lh.ces.mgh Then use “mri_surf2surf”, “mri_glmfit” to do the group analysis. My second question is: does the following two procedures both feasible for fMRI group analysis ? Isxconcat-sess —> mri_glmfit —> mri-glnfit-sim mris_preproc —> mri_surf2surf —> mri_glmfit —> mri-glmfit-sim Thank you! Regards, Star ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
