Re: [Freesurfer] Coordinates in TRACULA group analysis

Hi Anastasia, There is an error in .log files of left corticospinal tract in cvs template and I attached one of file. In addition .log files of right corticospinal tract in cvs template doesn't exist. Thanks in advance. Anri **

[Freesurfer] V3A ROI?

Dear experts, I am trying to find a probabilistic map of the visual cortical area V3A. I have not been able to find this particular area in the standard atlases in FSL or FreeSurfer. The Jülich Histological atlas contains a V3V ROI but not V3A. Do any of you know have this ROI as a file or do you

Re: [Freesurfer] right hemisphere specific problem with converting labels from fsaverage to subject space

I’m having issues with the conversion of labels drawn in fsaverage to subject’s space (using mri_label2label). I’ve manually drawn labels (V1-bins) in the fsaverage brain in both the left and right hemisphere that I want to convert to a subjects brain. I’ve successfully managed to do this for t

Re: [Freesurfer] V3A ROI?

Wang, Mruczek, Arcaro, Kastner (2014). Probabilistic Maps of Visual Topography in Human Cortex. Cerebral Cortex, Oct;25(10):3911-31 2016-07-11 12:13 GMT+02:00 Anders Hougaard : > Dear experts, > > I am trying to find a probabilistic map of the visual cortical area V3A. > I have not been able to

[Freesurfer] longitudinal qdec tables

Dear FreeSurfer Developers and Community, I have been trying to run some commands using the -qdec-long flag (I.e. asegstats2table & mris_preproc) but am encountering errors. In the past I have used .rtf files to read in my data using the -fsgd flag but am unsure of how to go about this with lon

Re: [Freesurfer] longitudinal qdec tables

Hi Derek, For debugging try a simple file with two lines (header and first row). Separate columns only with a space. Once that works add more rows. Best Martin On Jul 11, 2016 12:58 PM, "Andrews, Derek" wrote: Dear FreeSurfer Developers and Community, I have been trying to run so

Re: [Freesurfer] right hemisphere specific problem with converting labels from fsaverage to subject space

sorry, forgot to respond earlier. Which V1 label are you using? You might try thresholding it to remove the low-probability vertices that make it larger than it should be cheers Bruce On Mon, 11 Jul 2016, Halbertsma, HN (ohk) wrote: I’m having issues with the conversion of labels drawn in fs

Re: [Freesurfer] V3A ROI?

no, sorry, we don't have that data. If you ask the authors for it we would be happy to distribute it with FS if they are willing. cheers Bruce On Mon, 11 Jul 2016, Francesca Strappini wrote: Wang, Mruczek, Arcaro, Kastner (2014).  Probabilistic Maps of Visual Topography in Human Cortex. Cere

[Freesurfer] mri_glmfit-sim

Dear Freesurfers, As freesurfer mri_glmfit-sim is based on AlphaSim & FSL randomise, I would like to know if the results I’m getting are affected by recently found bugs/violations in RFT assumptions, e.g. http://www.pnas.org/content/early/2016/06/27/1602413113.full.pdf. Thank you in advance! La

Re: [Freesurfer] V3A ROI?

Excellent, thank you. The link to the ROI files is this: http://www.princeton.edu/~napl/vtpm.htm Best, Anders 2016-07-11 12:26 GMT+02:00 Francesca Strappini : > Wang, Mruczek, Arcaro, Kastner (2014). > Probabilistic Maps of Visual Topography in Human Cortex. > Cerebral Cortex, Oct;25(10):3911-31

[Freesurfer] When I am run trac-all in Fedora 24 with the developmental version of FreeSurfer, it crashes when running flirt.fsl with this error message

flirt.fsl -ref/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/refvol.fslregister.nii-in/home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/movvol.fslregister.nii-bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90-searchrz -90 90 -verbose

Re: [Freesurfer] longitudinal qdec tables

Hi Martin, Thank you for the tip. Indeed there is some issue with the character spacing in my qdec file. I usually generate subject text files like this in excel and save them as csv .txt files. Do you have any suggestions for easily writing the qdec file without going line by line, space by s

Re: [Freesurfer] longitudinal qdec tables

So you exported CSV from excel on Mac with space separation and it does not work? Try to export only a few lines to make sure it is not a weird character somewhere else. Best Martin On Jul 11, 2016 5:44 PM, "Andrews, Derek" wrote: Hi Martin, Thank you for the tip. Indeed there is

Re: [Freesurfer] V3A ROI?

Hi Anders thanks. Seems like you can just get the data from them and are all set. Bruce On Mon, 11 Jul 2016, Anders Hougaard wrote: Excellent, thank you.The link to the ROI files is this: http://www.princeton.edu/~napl/vtpm.htm Best, Anders 2016-07-11 12:26 GMT+02:00 Francesca Strappini :

[Freesurfer] tcsh update

Dear FS experts: I am running FS in local computer and showing following error message and program stopped at recon-all WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Do I need to update tcsh? and how can I do it. thanks Lawrence ___

[Freesurfer] mri_glmfit error: Matrix is ill-conditioned or badly scaled

Hi Freesurfer Experts, I am trying to run mri_glmfit and while 90% of my files work, some of them display the error below. I have tried demeaning, and then tried multiplying this value by 100, and I still get the same error. Any feedback would be greatly appreciated. mris_preproc done srcsubjec

Re: [Freesurfer] Regarding: Concatenating hippocampal to generate sig.mgh

Dear Bruce, Thanks for you for your response. I am trying to generate an average hippocampal volume and its correlation with HAM-D score in early and late onset depression (eod vs lod). One way I tried to do it was by binarizing and concatanating the hippocampal volumes and then run mri_glmfit. B

[Freesurfer] R: Re: Recon-all error after El Capitain update

This is the command and the error line. Thanks. Stefano recon-all -all -i $SUBJECTS_DIR/T1_STRUCT.nii.gz -subject SUBJECTS_DIR # INFO: fsaverage subject does not have perirhinal labels! \n cd /Applications/freesurfer/subjects/subject_prova/Control89;