[Freesurfer] BA lable Error

Hi, Recon-all has error at BA Labels stage. how can i run it from this stage again. I need cortical thickness, Do i need to run it? Kind Regards, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinf

Re: [Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04

Thanks Doug! What is the estimated time for the release of Freesurfer/FS-FAST stable version 6, including a documentation to use it with freeview? Reza The new version of fsfast will use freeview for tksurfer/tkmedit/tkregister. In 5.3, you can use tkmeditfv and/or add -freeview to the tkmedit-s

Re: [Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04

Thanks Zeke! I have replicated this problem in at least three machines running Ubuntu 14.04. Reza Hello Reza, I wasn't able to replicate on Ubuntu 12 but it's entirely possible this but exists only in Ubuntu 14. It's tough because we don't have test machines with every Linux distro that peop

Re: [Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04

Hello Reza, I wasn't able to replicate on Ubuntu 12 but it's entirely possible this but exists only in Ubuntu 14. It's tough because we don't have test machines with every Linux distro that people post to the list about in order to attempt replicate. But I'll install Ubuntu 14 on a laptop afte

Re: [Freesurfer] Longitudinal Freesurfer | BA labels does not change

Hi Pradeep, I just checked an example (using FS 5.3) and there my BA.stats do change across time points in the longitudinal stream. So maybe - you input identical images into the individual time points? - you looked at the same file? - maybe some other processing error (e.g. same name for diffe

Re: [Freesurfer] help on mris_preproc

Hi Doug, Thanks. I can see that the "mris_preproc" command reads the header information in "register.dat". I set the "." as the $SUBJECTS_DIR, and thus it seems that "mris_preproc" cannot locate the path. Is there a way to fix this? David Here is the (part of) output: -- end while ( $#

[Freesurfer] Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity

Hi list, I working on the combination of MRS and FS-FAST analysis.I have extracted the grey matter within voxel (I will call it "ROI_MASK") by using FSL tools and now it is in the same space of orig.mgz (the roi mask is perfectly overlapped on orig.nii.gz when I use fslview). I'd like to import

Re: [Freesurfer] recon-all complete in 10 hours!!!!

Hi Hassan those numbers seem reasonable. If there is a big problem it will frequently take very long (due to giant topological defects) cheers Bruce On Fri, 12 Jun 2015, Hassan bakhshi wrote: Hi all, "Recon-all  complete in 10 hours,should i be concerned?"  I asked this question before,

Re: [Freesurfer] help on mris_preproc

Can you run the 2nd command with --debug as the first option and send the terminal output? doug On 6/12/15 12:09 PM, David C. Zhu wrote: Dear FreeSurfer experts: I have been using FreeSurfer for segmentation and for volumetric analyses. I want to give a try to use it for surface-based fMRI a

[Freesurfer] recon-all complete in 10 hours!!!!

Hi all, "Recon-all complete in 10 hours,should i be concerned?" I asked this question before, and Bruce said depend on your computer it is acceptable. i checked the hardware, I use virtual box which has 5 cores of cpu and 4GB of RAM. i ran 2 instance of recon-all and both finished within 10 hour

[Freesurfer] help on mris_preproc

Dear FreeSurfer experts: I have been using FreeSurfer for segmentation and for volumetric analyses. I want to give a try to use it for surface-based fMRI analyses. I encountered some issues with mris_preproc to assemble IRF results to the fsaverage surface. Please advise on how to resolve these

[Freesurfer] Nifti surface files

Hi all, I'm trying to improve Python handling of FreeSurfer-generated .nii surface files (https://github.com/nipy/nibabel/pull/315). If I'm reading load_nifti.m (https://code.google.com/p/fieldtrip/source/browse/trunk/external/freesurfer/load_nifti.m) and load_nifti_hdr.m correctly, there are thr

Re: [Freesurfer] WM Edits not updating in batch

Hi Matt, Could you upload that subject to our filedrop and I will take a look. https://gate.nmr.mgh.harvard.edu/filedrop2/ -Allison On 06/12/2015 01:04 AM, Matthew Peverill wrote: (I'm working with Kate on this one) The problem is with the white matter surface. The pial surface is usually

Re: [Freesurfer] Timecourses In freesurfer

sorry, what time course? On 6/9/15 11:11 AM, jonathan oron wrote: Hi Doug, I think I've realized what the problem is - my cespct file has only one frame How can I run mkanalysis-sess, mkcontrast-sess and selxavg3-sess in a way that produces the whole percent signal change time course? Thanks

Re: [Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04

The new version of fsfast will use freeview for tksurfer/tkmedit/tkregister. In 5.3, you can use tkmeditfv and/or add -freeview to the tkmedit-sess command line. I've put the 6.0 versions of tksurferfv and tksurfer-sess here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tksurferf

Re: [Freesurfer] Tksurfer and Tkregister2 in Ubuntu 14.04

Hi Bruce, I guess I will eventually move to freeview - though I am not quite sure if it is easy to use with FS-FAST. For now, all features of tksurfer/tkmedit/tkregister2 work fine for me, except the one described below. So it would be great if this bug, that is specific for ubuntu, is resolved

Re: [Freesurfer] bad magic number

Hi Matthew, I'll send you two header files of affected scans by private e-mail. I heard the tool is being upgraded to use nibabel v2.0, but we haven't been able to test if the problem is still present in the latest version. Regards, Jalmar On Jun 11, 2015, at 06:47 PM, Matthew Brett wrote: