[Freesurfer] Tracula - configuration file error

Dear all, I am facing an error at the configuration file for trac-all I am trying to run a single subject, 148, for who there is a folder ‘148’ with all DWI DICOMs and a folder ‘ESNA148’ with the recon-all processing (Freesurfer 5.3). Also in $SUBJECTS_DIR there is bval.bval and bvec.bvec. I at

Re: [Freesurfer] Registration and Surface flatten

Hi Doug, Thanks for your suggestion on tksurfer, it works. I would like to map all the subjects into a flat map because I am curious about the 2-D thickness patterns between different groups. I think there will be some distinctions. But if I flatten fsaverage, how can I map everyone’s 3D surface

Re: [Freesurfer] normalization problem (versions 5.1 and 5.3)

Hi Maia Yes, it's possible. We've made a bunch of improvements Bruce > On May 15, 2014, at 1:13 PM, Maia Pujara wrote: > > To follow up, it makes sense that the noise might be an issue, but it seems > like version 5.3 creates the surfaces just fine regardless of the noise, so > I'm wondering i

Re: [Freesurfer] A newbie to fMRI analysis

You are using with the extension .mgz thats wrong try: recon-all -s s600a1001 -all and as Markus suggests, use the -s flag for the subject directory Hth, Es On Thu, May 15, 2014 6:00 pm, Dr Sampada Sinha wrote: > Hello Shantanu, > > Thanks for your mail, but the error is still the same: > > Las

Re: [Freesurfer] A newbie to fMRI analysis

remove the quotation marks from '-all' and try again e.g. recon-all -s s600a1001.mgz -all Hth, S. On Thu, May 15, 2014 2:55 pm, Dr Sampada Sinha wrote: > Hello Shantanu I tried to set up the Subject directory using this command > and it says the following error: > > Last login: Thu May 15 14:49:

Re: [Freesurfer] Longitudinal Error: long_mris_slopes

Hi Jennifer, I have never tested if the long_...slopes commands work when the data was processed with an old FS version. And 4.5 is very old. I'd recommend you re-run the data with 5.3 as sooo much has changed in the longitudinal pipeline since then. Independent of that, do you have write pe

Re: [Freesurfer] A newbie to fMRI analysis

Hello Shantanu I tried to set up the Subject directory using this command and it says the following error: Last login: Thu May 15 14:49:50 on ttys000 dhcp020-222-214:~ sampada$ export FREESURFER_HOME=/Applications/freesurfer dhcp020-222-214:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh ---

[Freesurfer] Longitudinal Error: long_mris_slopes

Hello, I recently installed FreeSurfer v5.3 on a Mac OS X 10.9.2. I am trying to run a longitudinal analysis (longitudinal two-stage model) on my data (26 participants, 2 time points each) which was processed (cross-sectionally and longitudinally) using a previous version of FreeSurfer (v4.5). W

Re: [Freesurfer] aseg.stats volume mismatch

Hi Gabor the partial volume estimates are not the probabilities. We could output p-values, but that won't give you partial volume estimates. Bruce On Thu, 15 May 2014, Gabor Perlaki wrote: Dear Bruce, I think of a probability map for each segmented structure, like the partial volume images

Re: [Freesurfer] aseg.stats volume mismatch

Dear Bruce, I think of a probability map for each segmented structure, like the partial volume images for WM, GM and CSF in FSL. Is there anything like that in Freesurfer? Thanks, Gabor 2014-05-09 22:48 GMT+02:00 Gabor Perlaki : > Dear Bruce, > > I think of a file which also shows the partial v

Re: [Freesurfer] normalization problem (versions 5.1 and 5.3)

To follow up, it makes sense that the noise might be an issue, but it seems like version 5.3 creates the surfaces just fine regardless of the noise, so I'm wondering if perhaps there has been a chance in preprocessing before the end of the T1.mgz computation that solves the problem. Would there ha

[Freesurfer] Problems with tkmedit

Hi, I'm Esteve Cervantes an student from UPC. I'm trying to install Freesurferfrom the source and I'm having some problems with tkmedit. I previously had some problems with recon-all because I got segmentation faults. After installing the mni.srcbuilt.tgz from source and some fixes it runs ok. Bu

[Freesurfer] Tksurfer will not accept key input in Ubuntu 14.04

Bug report I am unable to enter number using the keyboard when using Tksurfer under Ubuntu 14.04. I have tried to enter a number in overlay configuration and smooth overlay. Is there any workaround? I have this bug on two different system with Ubuntu 14.04. Best regards Knut J Bjuland ___

[Freesurfer] BrainMask Edits

Question regarding the use of skull stripping errors. I am wondering if it is possible to correct (use the -wsthresh or -gcut) in longitudinal processed data or would these types of edits be required in the earlier processing steps (initial FreeSurfer recon-all)? Thanks in advance for any help

Re: [Freesurfer] white matter surface (tkmedit -surfs) vs wm.mgz

Hi Kristina sorry, I'm not sure I understand. The surfaces are the same or they are not the same? If you have edited the wm.mgz they should *not* be the same in general. The surfaces to examine are the lh.white and rh.white cheers Bruce On Thu, 15 May 2014, Mayer Kristina wrote: > Dear Bruce