[Freesurfer] Correcting defect problem after checking skull stripped and editing wm.mgz

External Email - Use Caution Dear freesurfer experts, When executing recon-all in two subjects with brain lesions, the recon-all process stopped at CORRECTING DEFECT 13 (vertices=49319, convex hull=12973, v0=65403) and CORRECTING DEFECT 6 (vertices=23529, convex hull=6740, v0=1602

[Freesurfer] error while running "-hippocampal-subfields-T1" with Freesurfer 6.0

External Email - Use Caution Hi, I have already run recon-all with default options on a large set of T1-weighted images, using Freesurfer v 6.0. Now we want to extract the hippocmpal subfields from these already processed images. Apparently our installation was missing Matlab Co

Re: [Freesurfer] Morphological Features, Description & References

External Email - Use Caution Hi you two, thank you very much for your quick reply! Just two short followup questions: @Bruce: Is this published in any paper or documentation so I can cite it? @Doug: Has this method been implemented with the last release of FS in 6.0.0 or alread

Re: [Freesurfer] Correcting defect problem after checking skull stripped and editing wm.mgz

Hi Jiun-Wei have you looked at the ?h.defect_labels overlaid on the inflated.nofix and orig.nofix surfaces? That will tell you where the defect is that is causing you trouble. If you have lesions they may be the source of the issue. If you can't sort it out you can tar and gzip the entire subj

Re: [Freesurfer] error while running "-hippocampal-subfields-T1" with Freesurfer 6.0

Hi Shahrazd can you try: chmod -R a+rx $FREESURFER_HOME/bin and see if that fixes your problem? Bruce On Mon, 9 Sep 2019, shahrzad kharabian wrote: External Email - Use Caution Hi,  I have already run recon-all with default options on a large set of T1-weighted images, u

Re: [Freesurfer] Morphological Features, Description & References

for the continuous curvature you can just cite the FreeSurfer paper, or recon1/2). For the discrete curvature I think Rudolph Pienaar published something on it. Some of the curvature indices are from David Van Essen's papers, and the volume/area calculation is Anderson M. Winkler's paper chee

[Freesurfer] fspalm error

Hello Freesurfer community! I am trying to run fspalm on surface based data. I have installed PALM, fspalm, mri_surfcluster, and mri_volcluster. This is my fspalm command: fspalm --glmdir TEPSC.glmdir --cft 1.3 --twotail --name palm-twotail-1.3 --iters 1000 --2spaces --cwp .05 When I run the f

Re: [Freesurfer] Extracting contrast data from mri_glmfit to graph

Right, the ocn.dat files have data that is uncorrected in that sense and might need to nuisance factors removed before plotting. There is a design matrix in there (Xg.dat). You can load that into matlab along with the ocn.dat, compute beta = inv(X'*X)*(X'*ocn) to get the betas. You can then comp

Re: [Freesurfer] fspalm error

I think palm itself requires mgh or mgz files. I can't remember why we don't convert it. You can run mri_glmfit with --mgz or --mgh (or just without --nii.gz) and it should work. On 9/9/2019 9:24 AM, Barbour, Tracy,M.D. wrote: Hello Freesurfer community! I am trying to run fspalm on surface ba

[Freesurfer] Opseq2 question

Hi Freesurfer experts I have a question about designing an event related task. We are designing a task for fear conditioning. Each stimuli presentation lasts 4 seconds. My question is if we set the TR to 2 (which is a multiply of 4), will it make the paradigm to have more power in signal detect

Re: [Freesurfer] Extracting contrast data from mri_glmfit to graph

External Email - Use Caution Hi Douglas, That's good to know its still a form of voodoo correlation. If researchers wanted to avoid this, when looking for an interaction effect in a DODS model with a continuous variable yet still wanted to know the direction of the relationships h

[Freesurfer] Issue downloading FS-FAST fMRI tutorial data

External Email - Use Caution Hello there, When attempting to get the analysed functional data using the below command: wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-functional.tar.gz I get the following OUTPUT error: --2019-09-09 14:21:20-- ftp://surfer.nmr.mgh.harvard.

[Freesurfer] freesurfer 6.0 hires fix

External Email - Use Caution I noticed that you guys released a fix to improve the -hires option. I have been processing some of our data using the hires flag. if i use this fix do i need to run recon-all from the beginning or can I run over the old folders? __

Re: [Freesurfer] freesurfer 6.0 hires fix

You have to rerun from the beginning. (sorry) On 9/9/19 3:12 PM, Aaron Tanenbaum wrote: > > External Email - Use Caution > > I noticed that you guys released a fix to improve the -hires option.  > I have been processing some of our data using the hires flag. if i use > this fix do i need

Re: [Freesurfer] Extracting contrast data from mri_glmfit to graph

It is voodoo to do the same test that you used to generate the cluster (or have a graph that implies such a test). If you want to do a post-hoc test, that is totally fair. Eg, if you do an unsigned test between the two groups, you could then go back and do a signed test on the extraction. On

Re: [Freesurfer] Issue downloading FS-FAST fMRI tutorial data

External Email - Use Caution There should be a file there now, so please try it again. - rob On Sep 9, 2019, at 14:26, Rami Hamati wrote:External Email - Use CautionHello there,When attempting to get the analysed functional data using the b

Re: [Freesurfer] Issue downloading FS-FAST fMRI tutorial data

External Email - Use Caution Thanks, it worked. Cheers, Rami On Mon, Sep 9, 2019, 16:04 fsbuild wrote: > External Email - Use Caution > > There should be a file there now, so please try it again. > > - rob > > On Sep 9, 2019, at 14:26, Rami Hamati wrote: > > E

Re: [Freesurfer] Issue downloading FS-FAST fMRI tutorial data

External Email - Use Caution Hey Rob, I have the same issue for the following command: wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gz If you could add that file too, that would be great. Rami On Mon, Sep 9, 2019 at 4:04 PM fsbuild wrote: >

[Freesurfer] Convert nifti atlas into .annot file

External Email - Use Caution Dear all, How can i create .annot files for both left and right hemisphere from nifti atlases http://www.gin.cnrs.fr/en/tools/aal/ are there any specific guidelines or commands for surface based parcellation ? Thanks Vasudev

Re: [Freesurfer] Issue downloading FS-FAST fMRI tutorial data {Disarmed}

External Email - Use Caution OK, give it another try. - R. I have the same issue for the following command:wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/fsfast-tutorial.subjects.tar.gzIf you could add that file too, that would be great.RamiOn Mon, Sep 9, 2019 at 4:04 PM fsbuild

Re: [Freesurfer] Correcting defect problem after checking skull stripped and editing wm.mgz

External Email - Use Caution Hi Bruce Thanks so much for your quick reply. I had overlaid the ?h.defect_labels on the inflated.nofix and orig.nofix. I adjusted the threshold to focus on the largest defect. Although I could look at the defect, I couldn't figure how to fix it manual

Re: [Freesurfer] [FREESURFER] longitudinal processing base_tmps does not exist error

Hi Seonjoo, your base command is missing the "-all" so no processing is done in the base, which is why the file is missing later.. Best, Martin On Wed, 2019-08-07 at 17:27 +, Lee, Seonjoo wrote: > External Email - Use Caution > Dear Freesurfer, > Could you help me to resol