Re: [Freesurfer] (no subject)

External Email - Use Caution Hi Doug, I ran mri_glmfit \--table aseg.txt \--fsgd newCH_deblank3.fsgd dods \--C groupdiff.mtx \--glmdir aseg.glmdir this created a folder aseg.glmdir which contains another folder groupdiff, where sig.ghm is, I then tried to visualise results using

[Freesurfer] Error/shifting in cortical parcellation

External Email - Use Caution Dear Freesurfer Community, I wish to manually reassign/edit cortical parcellation performed by FS. We use the cortical parcellation done by FS and it has worked very well for most of our subjects. However, we have two subjects where the parcellation

Re: [Freesurfer] recon-all errors

External Email - Use Caution Thanks. I've never used this command before to register the FLAIR, but I'm getting the following error: [mwagshul@loginnode2 mri]$ tkregisterfv --mov orig/FLAIRraw.mgz --reg transforms/FLAIRraw.lta --targ orig.mgz cd /gs/gsfs0/users/mrrc-all/PROJECT

Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)

External Email - Use Caution Thank you for your help ! I have run the command: mri_nu_correct.mni --debug --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 >& nucor.log and got the nucor.log. -原始邮件- 发件人:"Douglas N. Greve" 发送时间:2021-06-

Re: [Freesurfer] PVC to calculate myelin maps

External Email - Use Caution Thank you very much for your response Doug. What PVC method is most recommended to use to calculate the T1 / T2 ratio (RBV or MG)? And what value of PSF should we specify to calculate this ratio? To my knowledge, this is an acquisition related paramete

Re: [Freesurfer] recon-all errors

External Email - Use Caution It works fine in 6.0, was in 7.1. The registration looks fine (the FLAIR is brain extracted, while the orig.mgz is not, is this expected, or was that my error, I don't recall which FLAIR image I fed in). Mark Mark Wagshul, PhD A

Re: [Freesurfer] Freesurfer- subcortical group analysis

There are not results to visualize, there is just a table. There should be a sig table in the output folder On 5/28/2021 9:37 AM, Aldinhas De Freitas Ferreira, Francisca wrote: External Email - Use Caution So so sorry to bother you again - hopefully the last time... I have followed y

[Freesurfer] OHBM Brainhack 2021

External Email - Use Caution Dear all, We are happy to announce the upcoming Organization for Human Brain Mapping (OHBM) Brainhack 2021 happening June 16-18 around the clock around the world! Join the party by registering here

Re: [Freesurfer] mris_fix_topology taking ages

External Email - Use Caution Hi Doug, when you say it did not finish, could you clarify what process "it" refers to? I loaded the files you suggested and nothing popped out to me aside from the fact that the wm.mgz didn't seem to cover all the white matter. Is it possible that top

Re: [Freesurfer] mri_glmfit-sim with grf (ERROR: need --csd with --csd-out)

look at the tutorial On 6/1/2021 12:00 AM, Diógenes Bispo wrote: External Email - Use Caution I would like to know what other modification I should make to my script to run --grf (volume analysis): - mris_preproc ?? - mri_glmfit (--surf in white) - mri_glmfit-sim ?? Thanks. Diogen

Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)

What happens when you run the following two commands? echo 5/6 | bc -l echo "5/6" | bc -l On 6/1/2021 9:59 AM, liub wrote: External Email - Use Caution Thank you for your help ! I have run the command: mri_nu_correct.mni --debug --i orig.mgz --o nu.mgz --uchar transforms/talairac

Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)

Actually, I think I see what the problem is. You apparently have a command called "bc" in your path. mri_nu_correct.mni is trying to use the linux-native bc command (a simple calculator usually located in /bin). What do you get when you run which bc On 6/1/2021 9:59 AM, liub wrote:

Re: [Freesurfer] PVC to calculate myelin maps

On 6/1/2021 10:19 AM, Marina Fernández wrote: External Email - Use Caution Thank you very much for your response Doug. What PVC method is most recommended to use to calculate the T1 / T2 ratio (RBV or MG)? I've never done it before. I usually use MG (this will only work for gray ma

Re: [Freesurfer] mris_fix_topology taking ages

I mean mris_fix_topology. Try loading the ?h.smoothwm.nofix in surface viewing (not in the volume). You can often see defects better on this surface (they look likes holes or handles; you should at least see some) On 6/1/2021 4:55 PM, Ellen Ji wrote: External Email - Use Caution Hi D

Re: [Freesurfer] recon-all errors

OK, I'll have to take a look at the data. Someone will be in touch about getting it. On 6/1/2021 11:02 AM, Mark Wagshul wrote: External Email - Use Caution External Email - Use Caution It works fine in 6.0, was in 7.1. The registration looks fine (the FLAIR is brain extract

Re: [Freesurfer] Freesurfer- subcortical group analysis

External Email - Use Caution I see, thanks. Is there a way in Freesurfer to obtain a visual representation of these results- like in other modalities of group analysis? (eg. surface based) Many thanks On Tue, 1 Jun 2021 at 17:44, Douglas N. Greve wrote: > There are not results

Re: [Freesurfer] Freesurfer- subcortical group analysis

Not easily. You can do something in matlab, eg, aseg = MRIread('fsaverage/mri/aseg.mgz'); out = aseg; out.vol = zeros(out.volsize); ind = find(aseg.vol==17); % 17 = left hippo out.vol(ind) = YourValueForLeftHippoFromTheGLMAnalysis; % same thing for other ROIs MRIwrite(out,'sig.aseg.mgz'); Then vi

Re: [Freesurfer] mris_fix_topology taking ages

Or the ?h.inflated.nofix can be helpful as well From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Tuesday, June 1, 2021 5:57 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_fix_topology taking ages I mean mris_fix_topology. Try loading the ?h.

[Freesurfer] FW: [All] Postdoctoral position at the Multicultural Alzheimer's Prevention Program

Contact Dr. Quiroz If you are interested in the postdoc opportunity below Bruce From: all-boun...@nmr.mgh.harvard.edu On Behalf Of Quiroz, Yakeel T.,Ph.D. Sent: Tuesday, June 1, 2021 8:44 PM To: a...@nmr.mgh.harvard.edu Subject: [All] Postdoctoral position at the Multicultural Alzheimer's Prev