Re: [Freesurfer] GLM: Error Matric-Scale

Dear Douglas, The file is created on a mac using the open -e command. I’ve tried running your command: cat whiplash.fsgd | sed 's/\r/\n/g' new.whiplash.fsgd However, this makes the file unreadable for FreeSurfer. Any ideas? Thank you in advance, Robby Date: Thu, 21 Aug 2014 13:30:19 -0400

Re: [Freesurfer] Some notes on getting Tracula to work for newbies

Hi Kirstie - Your work-around works, but I should've actually included the new mri_convert in the update. I've included it now, so you'll find it if you download the last tracula update again. This should make things run smoothly without changing any scripts. Let me know if this solves it

Re: [Freesurfer] tracula: bvec-error

Hi Robby - It looks like in your config file setbveclist is one word, instead of set bveclist. This may be why you're getting the Badly placed ()'s. error at the very beginning of your trac-all output. And it would explain why it can't find the files. Hope this helps, a.y On Thu, 21 Aug

[Freesurfer] Crash

Hi all, hope this email finds you well. I am a new user of this program. I tried to open lh.thickness opening a load surface but the program continues to crash. Please can you help me? Lucio Lucio D'Anna PhD Research Student Forensic Neurodevelopmental Science Department Institute of

Re: [Freesurfer] brainmask error

Hi Bruce (and the rest of the list), It looks better (see attached) but it still look like it removed too much. cheers for the point though, Mads On 21/08/14 16:22, Bruce Fischl wrote: Hi Mads what does it look like if you move off the mideline? Or check a coronal view? Sagittal views of the

Re: [Freesurfer] Correlation of symptom severity and significant clusters

Dear Doug, I am using the current version of free surfer (5.3.0). Unfortunately there isn't a file with the same/similar name. Do you think it should exist in 5.3.0? Best Katharina 2014-08-19 17:19 GMT+02:00 Douglas Greve gr...@nmr.mgh.harvard.edu: Yes, you are just getting the raw data

Re: [Freesurfer] tracula: bvec-error

Hi Anastasia Thanks for your quick reply. I’ve changed the command and I got one step further. Now I get another error: mv -f /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs mv: rename

Re: [Freesurfer] Crash

Hi Lucio, you need to give us more information. Try looking at this web site to find out what we need http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting On 8/25/14 7:03 AM, D'anna, Lucio wrote: Hi all, hope this email finds you well. I am a new user of this program. I tried to open

Re: [Freesurfer] Correlation of symptom severity and significant clusters

There won't be a filed called exactly that,but one of a name similar to that. Is there such a file. If you did the MC simulation in 5.3 and you had one or more significant clusters, then there should be. On 8/25/14 7:43 AM, Katharina Zech wrote: Dear Doug, I am using the current version

Re: [Freesurfer] brainmask error

Are you sure? Did you flip back and forth between this and a volume with the skull? On Aug 25, 2014, at 7:13 AM, Mads Jensen mje.m...@gmail.com wrote: Hi Bruce (and the rest of the list), It looks better (see attached) but it still look like it removed too much. cheers for the point

Re: [Freesurfer] Correlation of symptom severity and significant clusters

Also in case of a full mc simulation? I know that ocn files exist for precomputed mc simulations in qdec. Yes, I got version 5.3.0 and significant clusters. 2014-08-25 16:07 GMT+02:00 Douglas Greve gr...@nmr.mgh.harvard.edu: There won't be a filed called exactly that,but one of a name similar

[Freesurfer] International PhD Course in Molecular Medicine, Experimental Neurology Section, San Raffaele Hospital, Milan, Italy.

The Neuroimaging Research Unit, Vita-Salute San Raffaele University, Milan, Italy, headed by Prof. Massimo Filippi, is looking for graduate students interested in a three-year PhD program in the frame of the International PhD Course in Molecular Medicine, Experimental Neurology Section. Titles

Re: [Freesurfer] GLM: Error Matric-Scale

I don't know the open command. Try some other editor. Attached is what I get when I run the cat command below, and it reads fine into FS. On 08/25/2014 02:50 AM, Robby De Pauw wrote: Dear Douglas, The file is created on a mac using the open -e command. I’ve tried running your command:

Re: [Freesurfer] Correlation of symptom severity and significant clusters

Yes, i got several ones. Am Montag, 25. August 2014 schrieb Douglas N Greve : yes. Do you have significant clusters? On 08/25/2014 10:41 AM, Katharina Zech wrote: Also in case of a full mc simulation? I know that ocn files exist for precomputed mc simulations in qdec. Yes, I got version

[Freesurfer] head surface

Sorry about that, here is the whole correspondance: Hi Doug, I used mkheadsurf function. Meryem Hi freesurfer community, I am trying to get faces and vertices of the head surface mesh in Matlab. freesurfer_read_surf works perfectly when I extract faces and vertices for the pial surface

Re: [Freesurfer] tracula: bvec-error

Hi Robby - Which version of tracula are you using? In general it's hard to guess what's going on just by seeing the error message. Please attach the entire log file (scripts/trac-all.log). a.y On Mon, 25 Aug 2014, Robby De Pauw wrote: Hi Anastasia Thanks for your quick reply. I’ve

[Freesurfer] Tracula - May update version

I have a few questions about the May 2014 update to Tracula: 1. Between the 2013-12-04 trac-all version 1.53 and 2014-05-26 trac-all version 1.56, the longitudinal stream now uses the aparc+aseg.mgz from the *.long.* directories, and all output is saved there, too. Are the

Re: [Freesurfer] head surface

Is this what you are running? [vertex_coords, faces] = read_surf('lh.seghead'); When I run it, it runs fine under 5.3. Is that the version you are running? doug On 8/25/14 11:18 AM, Meryem Ayse Yucel wrote: Sorry about that, here is the whole correspondance: Hi Doug, I used mkheadsurf

[Freesurfer] Save ROIs/labels from mri_glmfit group analyses

Dear Surfers, In qdec, there is an option to draw a ROI (of a significant cluster) and save that ROI as a .label file. Does the command-line version, mri_glmfit, have an equivalent protocol? I have unsuccessfully tried to create these ROIs in Freeview (which for some unknown reason, has been

Re: [Freesurfer] Save ROIs/labels from mri_glmfit group analyses

I'm not sure how you are doing in qdec, but mri_glmfit-sim will create labels for each cluster, you will just need to set the voxelwise threshold appropriately, and you may need to set the cwp to something large (1 means to take all clusters no matter how small) doug On 8/25/14 11:11 PM,

[Freesurfer] Which Freesurfer regions in Default mode network ?

Hi Folks, I wanted to ask which Freesurfer regions from aparc+aseg.mgz are included in Default mode network ? Is there a relevant publication on this topic ? Thanks Mehul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Which Freesurfer regions in Default mode network ?

Hi Mehul, You can use the resting-state fMRI-defined default network regions in fsaverage space. See http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011. Note that the parcellation is now part of FreeSurfer official release. See relevant publication in wiki. Cheers, Thomas On