[Freesurfer] trac-all error

External Email - Use Caution Hello Freesurfer, After running recon all script which completed successfully, I ran trac-all command which exited with error and tried running it with dicom files. dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address

Re: [Freesurfer] Learning dti processing tutorial

Sorry, you will have to figure this out for yourself. On 10/18/2019 5:02 PM, Renew Andrade wrote: External Email - Use Caution I am using a database of NITRC repository https://www.nitrc.org/projects/parktdi/ . This images have a nifti file for 1000s/mm^2 and 2500s/mm^2. I don’t know

[Freesurfer] help

External Email - Use Caution ?Good afternoon, Is there any other way to incorporate a manually edited brain mask into the recon all process other than through the recon-mode in freeview? Thanks! Asim Hassan Research Technician II Waugh Lab Division of Pediatric Neurology

Re: [Freesurfer] Learning dti processing tutorial

External Email - Use Caution I am using a database of NITRC repository https://www.nitrc.org/projects/parktdi/ . This images have a nifti file for 1000s/mm^2 and 2500s/mm^2. I don’t know if it is MPRAGE or not. Can you help me? What

Re: [Freesurfer] Error in glmfit-sim cache

External Email - Use Caution I have tried all the values it pinpoints to but none seem to work. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Research Specialist Position on the MIDUS Neuroscience project's longitudinal study of aging, emotion, and well-being at the Center for Healthy Minds

External Email - Use Caution The Center for Healthy Minds at the University of Wisconsin-Madison is hiring a Research Specialist. The Research Specialist will be responsible for scientific integrity of data collection, data processing, and participant recruitment, screening,

Re: [Freesurfer] imperfect segmentation in the occipital lobe in epilepsy patient

External Email - Use Caution Dear Bram, Thanks very much for your help. If I am understanding correctly, you first filled the lesions in the wm (brain.finalsurfs.mgz) in freeview with 'voxel edit', brush value = 110. Then you recreated a new wm.mgz, with which commands? I might

Re: [Freesurfer] can´t open an image in Freeview

External Email - Use Caution Hello Adam, See if you can run the following command, and if it reports anything is not found (you can cut and paste the command) - R. $ ldd `which freeview` | grep not Adam RytinaOctober 18, 2019 at 14:31

Re: [Freesurfer] imperfect segmentation in the occipital lobe in epilepsy patient

Hi Xiaoqian, We don't typically recommend this, but it looks like you will need to edit your brain.finalsurfs.mgz to account for the wm lesion. I tested this out by filling in the lesion with 110 and recreating the wm surface -- it seems to work quite well. Once that is done, you can run the

[Freesurfer] Post-doc on multi-tracer PET-MRI

Hi everyone, My lab is looking for a post-doc. Please spread the below advertisement far and wide With my best regards Clas Linnman The Spaulding Neuroimaging Laboratory (PI Clas Linnman, assistant professor, Harvard Medical School), working closely with the Martinos Center for Biomedical

Re: [Freesurfer] Group effect Contrast for 6 groups

External Email - Use Caution Great thanks. On Fri, Oct 18, 2019, 10:09 AM Greve, Douglas N.,Ph.D., < dgr...@mgh.harvard.edu> wrote: > Yes, that is correct. It is testing the null hypothesis A=B=C=D=E=F. That > hypothesis will be rejected if A is different from B-F, which is what

Re: [Freesurfer] Mri_mask producing only zeros

Can you send the full command line (the one below does not make sense)? And send the terminal output On 10/14/19 11:53 AM, Sims, Sara A (Campus) wrote: External Email - Use Caution Freesurfers, I am trying to use mri_mask using surface overlays. I made a label into a volume and then

Re: [Freesurfer] brain mask without CSF ...

Not sure why you are getting the holes. There might be WM hypointensties that would not be captured by your model. I've put a new version of mri_binarize here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize You can also just use --match ID1 ID2 ... in the mri_binarize that you have

Re: [Freesurfer] covariate with repeated anova

I'm not sure how to do this in the RM ANOVA framework. Since you only have two time points, why not just compute their difference then use a typical design? On 10/11/19 2:34 PM, miracle ozzoude wrote: External Email - Use Caution Hello Experts, I would like to include covariates in

Re: [Freesurfer] Download link broken

Hi Tashrif, sorry, we had a network outage last night, but the link should be fixed now. best, Andrew From: on behalf of "Billah, Tashrif" Reply-To: FS Help Date: Friday, October 18, 2019 at 10:08 AM To: FS Help Subject: [Freesurfer] Download link broken Hi FreeSurfer team, The following

Re: [Freesurfer] Group effect Contrast for 6 groups

Yes, that is correct. It is testing the null hypothesis A=B=C=D=E=F. That hypothesis will be rejected if A is different from B-F, which is what you are testing. The other contrasts are redundant (and would cause an error if you added them to the contrast matrix)z On 10/16/19 12:03 PM, cody

[Freesurfer] Download link broken

Hi FreeSurfer team, The following link appears broken since 10/17 evening. https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz Can you look into it? Best, Tashrif -

Re: [Freesurfer] QDEC cluster output

Hi Lara, sorry, we don't really support qdec anymore for the very reason that we can't get into the code easily and answer these questions. Can you use the command-line stream? doug On 10/17/19 6:17 PM, Lara Foland-Ross wrote: External Email - Use Caution Hi Freesurfer experts, I’m

Re: [Freesurfer] ERROR gtmseg

Oh, yes, sorry. The problem was that you are using FS 5.1 segmentations and things have changed since then in a way that makes it incompatable with gtmseg. One possibility is to run gtmseg with --ctab $FRESURFER_HOME_51/FreeSurferColorLUT.txt If that does not work, you may need to reanalyze

Re: [Freesurfer] aseg.stats format FreeSurfer 5 versus 6

They are just different names On 10/17/19 11:52 AM, Tim Schäfer wrote: > External Email - Use Caution > > Dear fs experts, > > I'm parsing aseg.stats files for subjects to extract global brain measures > and noticed that at least 2 names changed from FreeSurfer 5.1 versus > FreeSurfer

Re: [Freesurfer] FSGD file formatting for Xhemi

What are you trying to test? Usually you don't have lh and rh in the same glm On 10/17/19 7:09 AM, Jose Graterol wrote: External Email - Use Caution Dear Freesurfer Community, I have a question regarding the formatting of the FSGD file while doing an analysis with Xhemi. First the --y