Re: [Freesurfer] problems of testing freesurfer

Hi Andrew, I have followed your suggestion and the error pop up like this: Xues-MacBook-Air:~ DannyDeng$ mkdir test_subjects mkdir: test_subjects: File exists Xues-MacBook-Air:~ DannyDeng$ export SUBJECTS_DIR=/path/to/test_subjects Xues-MacBook-Air:~ DannyDeng$

[Freesurfer] freesurfer@nmr.mgh.harvard.edu

Dear Freesurfer users, I have big issues performing recon-all into the freesurfer VirtualBox. I dont get any error but no files are created except the 0001.mgz. Here is what I get. WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Subject Stamp:

Re: [Freesurfer] Registration

Hi Bruce as you explain I did the registration somewhere else and now I have the labels_gca in my subject space. 1. is it possible to somehow import this file in freesurfer and run the rest of the analysis ? 2.my question in general is that : can I in anyway do any correction for aseg outputs

Re: [Freesurfer] QDEC

Do you have permission to read it? How was it created? On 11/8/17 1:18 AM, Kinzel, Phillipp wrote: Hi, I have problems loading project  files in QDEC. I get the following error: Loading data table /tmp/qdec_project_archive/qdec.table.dat... ERROR: could not open

Re: [Freesurfer] Registration

Hi Nazanin 1. The registration is only one step in how we do segmentation, so I wouldn't suggest just using it. If you can convert your registration to .m3z format and put it in the subjects transforms/talairach.m3z you could try running from there forward. 2. Yes, you can edit the aseg in

Re: [Freesurfer] freesurfer@nmr.mgh.harvard.edu

what is your command line? Please send the recon-all.log file On 11/8/17 5:24 AM, aurelie ponz wrote: Dear Freesurfer users, I have big issues performing recon-all into the freesurfer VirtualBox. I dont get any error but no files are created except the 0001.mgz. Here is what I get. WARNING:

[Freesurfer] preproc-sess with symbolic links

Hi all, I’m trying to run preproc-sess using symbolic links in my SUBJECTS_DIR but the program exists with error message: could not find session . Symbolic links work fine when I run recon-all for instance. Suggestion for a fix would be greatly appreaciated. Cheers! Laurio

Re: [Freesurfer] freesurfer@nmr.mgh.harvard.edu

On the first one, you have to add -all, otherwise it won't do anything On 11/8/17 11:51 AM, aurelie ponz wrote: Thank you Douglas for your quick response ! I used the *recon-all -i ' -subjid * Since it wasnt working I tried *recon-all -autorecon1 -i ' -subjid * and it worked for _SOME_ files

[Freesurfer] Merge Images

Could you please help me with my problem? I have a Nifti image with segmented white matter hyperintensity and a wparc image made at freesurfer. I want to know how I can know the names of the Nifti image areas, using a wparc as a location map. So, the problem is: identify all areas. I wanted an

Re: [Freesurfer] freesurfer@nmr.mgh.harvard.edu

Thank you Douglas for your quick response ! I used the *recon-all -i ' -subjid * Since it wasnt working I tried *recon-all -autorecon1 -i ' -subjid * and it worked for *SOME* files (including the T1) but I don't get the hl/rl.pial files. Then I tried the *autorecon2* on the sa;e data and it

Re: [Freesurfer] problems of testing freesurfer

When setting SUBJECTS_DIR, you have to specify the actual path to the “test_subjects” directory that you created. "/path/to/test_subjects" isn’t a real path on your computer. In your case, the path might be something like "/Users/DannyDeng/test_subjects” In recon-all, the -i flag is used to

[Freesurfer] longitudinal base error. (not a netCDF file)

Hello FreeSurfer, While running base step of the longitudinal pipeline, i got the following error (please see the rec-all.log file for more details). How do i solve this problem? Thank you Best, Paul recon-all.log Description: Binary data ___

Re: [Freesurfer] functional to anatomical registration

On 11/8/17 5:57 PM, David Beeler wrote: Hi freesurfer people, I'm trying to understand preprocessing a little better, especially registration of functional data to anatomical space. I am currently running everything in the volume, doing motion correction per-run and then pooling all the

[Freesurfer] functional to anatomical registration

Hi freesurfer people, I'm trying to understand preprocessing a little better, especially registration of functional data to anatomical space. I am currently running everything in the volume, doing motion correction per-run and then pooling all the runs in the session together for the first

Re: [Freesurfer] Merge Images

HI Cleudiana the value of the voxels in the nifti image should be indices that you can use to lookup names in $FREESURFER_HOME/FreeSurferColorLUT.txt is that what you want? cheers Bruce On Wed, 8 Nov 2017, Cleudiana Lima wrote: Could you please help me with my problem? I have a Nifti

Re: [Freesurfer] mris_preproc srcsurfreg Freesurfer 6.0

Dear Doug, Are there reasons why registering to my_subject_average (template defined from, say, average in a cross-sectional sample) can be better than registering to fsaverage? Thank you. Best, Chintan ___ Freesurfer mailing list

[Freesurfer] Repeated amygdala dev7-segmentation volumes do not correspond

Hi! I have done twice the analysis of amygdala segmentation (dev 7 version) with exactly same way. The volumes do not correspond each other and there is approximately 2mm3 difference in volumes randomly in either direction. Is this normal or is it something to do with the dev 7 version?

[Freesurfer] Creating cached versions of Xhemi registrations

Dear FreeSurfer Users, I'm using FreeSurfer version 6.0. I've processing subjects with recon-all and performed surface-based interhemispheric registration (via Xhemi at https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi). I want to run a GLM on the subjects Area and Thickness from the differences

Re: [Freesurfer] QDEC

Hi Douglas, thank you for your quick response. Yes, I have permission to read and write for the file. I modified the permission to be able to execute the file as well, but that didn´t change anything. I created the file through the qdec- GUI and didn´t have any problems while running the GLM.

Re: [Freesurfer] Local gyrification index - vertex-wise analysis values

Thank you so much! Can I also learn whether running vertex-wise analysis without GLM analysis in Qdec is possible or not? As I said, I will compare a single patient with a group of healthy controls, so GLM would not work. What would you suggest for this? Is it possible to extract lGI values

[Freesurfer] Postdoctoral Research Associate in neuroimaging/data science

A Postdoctoral Research Associate position is immediately open to work with the Network Neuroscience lab (dayanlab.web.unc.edu) at the Biomedical Research Imaging Center, University of North Carolina at Chapel Hill. The position is

Re: [Freesurfer] mris_pmake

Dear Surfer & Rudolph, Hi, I tried to run mris_pmake, but only got this message: I'm sorry, but an error condition has occurred. While I was checking on the options file, I couldn't access the options file. Does it exist? How can I use mris_pmake? I'm working with Vitaly Napadow, and I would