Re: [Freesurfer] mri_surf2surf --projfrac error: cannot spec both --sval-xyz and --sval

Dont use --trgicoorder. Also, smooth the input, not the output (ie, use --fwhm not --fwhm-trg). Don't use projfrac there (which will fix the --sval-xyz error). Your 2nd command looks the same as the first On 9/27/20 10:30 PM, 谢娆 wrote: External Email - Use Caution Hi, To begin with,

Re: [Freesurfer] extract morphology data

This is a bug. Try this cd $SUBJECTS_DIR/sub1/surf ln -s lh.sphere.reg lh.fsaverage5.sphere.reg ln -s rh.sphere.reg rh.fsaverage5.sphere.reg On 9/28/2020 3:55 AM, 姜黎黎 wrote: External Email - Use Caution Hello, my command line is mris_preproc --s ${subject} --hemi ${hemi} --meas ${me

[Freesurfer] Tracula error

Hi, I am trying to run trac-all using a configuration file for 30 subjects with longitudinal data, and keep getting the following errors: Too many ('s. ERROR: must specify as many DWI dicoms as subjects I looked through my file line by line and looked at similar posts on the archives but could

Re: [Freesurfer] How to draw streamlines and their corresponding ROIs using freeview {Disarmed}

Hi Zhiyuan, You can load .trk file from “Load Tract” menu in freeview. Mat format is not supported unfortunately. Best, Ruopeng On Sep 28, 2020, at 10:21 PM, Zhiyuan Yu mailto:z...@my.fsu.edu>> wrote: External Email - Use Caution Hi Ruopeng, Thanks for your answer! My streamlines ar

Re: [Freesurfer] voxel wise cortical thickness and subcortical volume

Not subcortical volume, you'll need VBM for that On 9/28/2020 7:01 PM, Zeng, Qi wrote: External Email - Use Caution Hi, Is it possible to use Freesurfer to extract global voxel-wise cortical thickness and subcortical volume? Thank you so much! Best, Qi ___

Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED] [WARNING: UNSCANNABLE EXTRACTION FAILED]RE: [EXTERNAL]Re: a question on Talairach transformation

Try adding -oc 0 0 0 to the mri_convert command line On 9/28/2020 12:55 PM, Yi Li wrote: External Email - Use Caution Hi Douglas, I ran mri_convert --apply_transform talairach.xfm brainmask.mgz brainmask.talairach.mgz But brainmask.talairach.mgz is all black. No error was thrown du

Re: [Freesurfer] preproc-sess - motion correction problem

I'm guessing that AFNI can't do MC on a 2d "volume" (MC is inherently a 3D operation). You can try turning off MC in preproc-sess with -nomc On 9/25/2020 11:56 AM, Nasr, Shahin,Ph.D. wrote: Hi Surfers,      I have faced an issue with preproc-sess and I appreciate your help.  I have a single s

[Freesurfer] LGI value extraction

External Email - Use CautionDear expert,I have used freesurfer v6.0 to calculate local Gyrification index ( LGI ). And  I have output the file named lh.pial_lgi and extracted the value of LGI by using the following command:> mris_anatomical_stats -a ${SUBJECTS_DIR}/S005/label/lh.apa

Re: [Freesurfer] LGI value extraction

That is really LGI. aparcstats2table just defaults to "thickness". But you should double check that the value you see in lh.aparc_lgi.stats is the same as in result_lgi_lh.txt On 9/29/2020 12:38 PM, 祝菲 wrote: External Email - Use Caution Dear expert, I have used freesurfer v6.0 to c

[Freesurfer] Fwd: Extraction of subject-wise values after permutation test !

External Email - Use Caution Dear Doug and FreeSurfer team, Any help with this on an urgent basis would be really appreciated. Sorry for being a little impatient :(. Thank you so much ! -- Forwarded message - From: Martin Juneja Date: Mon, Sep 28, 2020 at 5:42 PM

Re: [Freesurfer] extract morphology data

External Email - Use Caution Okay, thanks a lot! -原始邮件- 发件人:"Douglas N. Greve" 发送时间:2020-09-29 23:07:46 (星期二) 收件人: freesurfer@nmr.mgh.harvard.edu 抄送: 主题: Re: [Freesurfer] extract morphology data This is a bug. Try this cd $SUBJECTS_DIR/sub1/surf ln -s lh.sphere.reg lh.f

[Freesurfer] Regressing out gender

External Email - Use Caution Hello, I am currently attempting a paired t-test of subjects between two time points, regressing out the effects of age and gender. I am currently running the paired analysis tutorial, and have done the step of computing the differences between pairs u