[Freesurfer] From SUMA Dset file to Freesurfer file( overlay an gii file on fsaverage brain)

Dear Freesurfer experts, If you are not skilled in SUMA, you can directly skip to part 2. I have a trouble when I converted a SUMA dset file to Freesurfer file which can be overlayed on Freesurfer's fsaveraage brain. Part 1: converting SUAM dset file to Freesurfer gii file I followed the in

[Freesurfer] Clusterwise Correction for Multiple Comparisons

Hi, Doug and all, I have two quesiotns about clusterwise correction for multiple comparsion. I run 2 corrections,and commands are as follows: a. mri_glmfit-sim --glmdir g2v0.weight --cache 1.3 abs --cwpvalthresh .05 --2spaces b. mri_glmfit-sim --glmdir g2v0.weight --cache 1.3 pos --cwpvalthresh .

[Freesurfer] Questions about cluster-wise correction

Hi, all, I have two quesiotns about clusterwise correction for multiple comparsion. I run 2 corrections for one same result,and commands are as follows: a. mri_glmfit-sim --glmdir g2v0.weight --cache 2.0 abs --cwpvalthresh .05 --2spaces b. mri_glmfit-sim --glmdir g2v0.weight --cache 2.0 pos --cw

[Freesurfer] fsaverage cortex thickness

Hi, all, How to calculate the mean cortex thickness of fsaverage? Thanks! Wilder___ 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

[Freesurfer] Multiple comparision method

Hi freesurfer experts, Is there other methods for multiple comparison correction apart from Monte carlo simulation in Freesurfer? Thanks! zhiwei___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/list

[Freesurfer] Creat ROI from annotation file

Hi Freesurfer experts, I want creat some ROI masks or parcellation from Caret PALS_B12_Visuotopic.annot file in fsaverage's label folder. I used the command mri_label2vol, mri_label2vol --annot $Dir/label/lh.PALS_B12_Visuotopic.annot --temp $Dir/mri/T1.nii --fillthresh .5 --o PALS_B12_Visuotopic

Re: [Freesurfer] Creat ROI from annotation file

too so that you don't >overwrite aparc+aseg.mgz) > >doug > >On 11/24/2014 07:54 AM, wangzhiwei3233 wrote: >> Hi Freesurfer experts, >> I want creat some ROI masks or parcellation from Caret >> PALS_B12_Visuotopic.annot file in fsaverage's label folder. >

[Freesurfer] mri_surfcluster problem

Hi Freesurfer experts, I just want to try cluster level threshold by cluster size, but not by mc simulation. So I tried the command like : mri_surfcluster --in sig.nii.gz --subject fsaverage --hemi lh --annot aparc --sign pos --minarea 50 --sum area50.pos.cluster.summary --o area50.pos.

Re: [Freesurfer] mri_surfcluster problem

terminal output? On 12/2/14 8:01 AM, wangzhiwei3233 wrote: Hi Freesurfer experts, I just want to try cluster level threshold by cluster size, but not by mc simulation. So I tried the command like : mri_surfcluster --in sig.nii.gz --subject fsaverage --hemi lh --annot aparc --sign pos --m

[Freesurfer] taskreg with inconsistent regressor number

External Email - Use Caution Dear FreeSurfer experts, In my experiment, some subjects missed some trials and some not. I wish set the missed trials as an external regressor, however, mkanalysis-sess seems applying the same parameters for all subjects. In my understanding, -taskre

[Freesurfer] converting preprocessed surface functional data to volume

External Email - Use Caution Dear Freesurfer experts, I am going to do convert the preprocessed surface functional data to volume in fsaverage space so that I can used the processed data in SPM for further analysis, saying, beta series analysis. Because the trial nubmer is not sa

[Freesurfer] converting preprocessed surface functional data to volume

External Email - Use Caution Dear Freesurfer experts, I am going to convert the preprocessed surface functional data to volume in fsaverage space so that I can used the processed data in SPM for further analysis, for example, beta series analysis. I tried mri_surf2vol, it worked.

Re: [Freesurfer] converting preprocessed surface functional data to volume

data come from? Are you trying to map the time >courses? That usually does not work that well as your resulting image >will be huge. One thing to do is to map it to a cropped volume (most of >the 256^3 is outside the brain) and or also map it to 2mm instead of 1mm. > >On 8/13/

[Freesurfer] No ROI name in summary of MNI305 group analysis

External Email - Use Caution Dear Freesurfer Experts, I did group-level analysis in MNI305 space. Then I output the summay via command 'mri_volcluster' as follows: mri_volcluster --in ./sig.nii.gz --thmin ${thvoxel} --sign ${sigsignTemp} --cwpvalthresh 0.05 --minsize 273 --fwhm

[Freesurfer] converting preprecessed functional surface data to gifti

External Email - Use Caution Dear Freesurfer experts, How can I convert the preprecessed functional surface data to gifti format(gii)? I tried mris_convert, but I encountered the following error. error: freadFloat: fread failed Your assistance would be highly appreciated.

Re: [Freesurfer] No ROI name in summary of MNI305 group analysis

; Subject: Re: [Freesurfer] No ROI name in summary of MNI305 group analysis To: freesurfer@nmr.mgh.harvard.edu Message-ID: Content-Type: text/plain; charset="utf-8" Try adding --reg $SUBJECTS_DIR/fsaverage/mri.2mm/reg.2mm.dat On 11/23/2023 2:32 AM, wangzhiwei3233 wrote: > &

Re: [Freesurfer] converting preprecessed functional surface data to gifti

To convert functional file, use ?-f ?. You also need to specify surface file. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of wangzhiwei3233 Sent: Friday, January 26, 2024 4:39 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] converting preprecessed functional su

[Freesurfer] cluster area from mri_surfcluster and read_curv are inconstant

External Email - Use Caution Dear Freesurfer experts, I got the area of a cluster by two methods, and found the results were inconstant. Method 1: During group level analysis, the individual surface was normalized to fsaverage. I exported the cluster area and label file by co