Re: [Freesurfer] ribbon.mgz, -1) : could not open file ERROR

Hi, Thank you. It seems to be working. The command returns, however, that there is nothing to be done in all three autorecons individually. What should that mean, considering the error in autorecon2? Regards Pedro Rosa On 21 Aug 2013, at 04:16 PM, Z K wrote: > Getting 'make' on Mac systems re

Re: [Freesurfer] Otto: unsupported slice timing pattern 5

Hi, One option is to open the volume in 3D Slicer and save it in .mgz format. 3D Slicer is free to download. John On 2013-08-22, at 4:30 PM, Otto Muzik wrote: > > Hi, > > I am trying to convert a SIEMENS T1-weighted volume to the mgz > format (via mri_convert) but I am getting constantly

[Freesurfer] Otto: unsupported slice timing pattern 5

Hi, I am trying to convert a SIEMENS T1-weighted volume to the mgz format (via mri_convert) but I am getting constantly the error message unsupported slice timing pattern 5 in file I saw in the archives that a lot of people had problems with this but could not find any solutions posted - w

Re: [Freesurfer] Problem with mris_ca_label (seg fault)

I do. You can look in the recon-all.log (or recon-all.cmd I think) and see if they are identical. If they are, make sure you are using the same binary On Thu, 22 Aug 2013, Demian Wassermann wrote: > How would I check this? > > I thought you meant when I run > > recon-all -autorecon-all -subjid c

Re: [Freesurfer] Problem with mris_ca_label (seg fault)

How would I check this? I thought you meant when I run recon-all -autorecon-all -subjid case01009 -i my_t1.nii.gz D -- Demian Wassermann, PhD dem...@bwh.harvard.edu LMI / PNL / SPL Labs Harvard Medical School Brigham and Women's Hospital 1249 Boylston, Boston, MA, USA http://lmi.bwh.harvard.e

Re: [Freesurfer] Problem with mris_ca_label (seg fault)

is the command line that recon-all runs exactly the same as what you run? On Thu, 22 Aug 2013, Demian Wassermann wrote: > Hi Bruce, > > No, but I was hoping not to have to run the whole process again (for all the > subjects I need to relabel) > > Thanks for the quick response > > D > -- > Demian

Re: [Freesurfer] Problem with mris_ca_label (seg fault)

Hi Bruce, No, but I was hoping not to have to run the whole process again (for all the subjects I need to relabel) Thanks for the quick response D -- Demian Wassermann, PhD dem...@bwh.harvard.edu LMI / PNL / SPL Labs Harvard Medical School Brigham and Women's Hospital 1249 Boylston, Boston, MA,

Re: [Freesurfer] Problem with mris_ca_label (seg fault)

Hi Demian does this happen if you run it through recon-all? Bruce On Thu, 22 Aug 2013, Demian Wassermann wrote: > Dear Support line of free surfer, > > I have a problem when I try to apply a new atlas to the surfaces. Even with > the standard free surfer atlases it segfaults > > Environment: >

[Freesurfer] Problem with mris_ca_label (seg fault)

Dear Support line of free surfer, I have a problem when I try to apply a new atlas to the surfaces. Even with the standard free surfer atlases it segfaults Environment: FREESURFER_HOME: /projects/schiz/software/freesurfer-v4.5/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub

Re: [Freesurfer] gradient table question for Tracula

I have GE data and never had to make any changes to the gradient table. On 08/22/2013 01:05 PM, Anastasia Yendiki wrote: Hi Sal - Sorry but I don't know what the interaction of dcm2nii and GE dicom headers is. If anyone else on the list uses dcm2nii on GE dicoms, they can chime in. To make

Re: [Freesurfer] gradient table question for Tracula

Hi Sal - Sorry but I don't know what the interaction of dcm2nii and GE dicom headers is. If anyone else on the list uses dcm2nii on GE dicoms, they can chime in. To make sure the gradient table is right, I'd always check the primary eigenvector directions (overlaying dmri/dtifit_V1.nii.gz on

[Freesurfer] Error message of Ubuntu 13.04 and Centos4 & Centos6

Dear Freesurfer experts, I installed FS Centos4-64(and also tried Centos6) on Ubuntu 13.04. I tried the commands in tutorial and got error message, listed as follows. Nevertheless, FS can read in volume and surface from GUI. Another question is, which one of Centos4 or Centos6 is more suitab

[Freesurfer] gradient table question for Tracula

Hi Anastasia, A question I had about the gradient tables for Tracula - I recently came across this passage from Hui Zhang: "To correct for any errors that you identify, you need to first modify the gradient table, then repeat the tensor reconstruction. The modification of the gradient table typic

Re: [Freesurfer] FW: FW: Contrast and F-test

Great!! Thank you so much! Heidi Dr. Heidi Jacobs Postdoc researcher Faculty of Health, Medicine and Life Sciences School for Mental Health and Neurosciences Division Cognitive Neuropsychiatry and Clinical Neurosciences Alzheimer Center Limburg h.jac

Re: [Freesurfer] FW: FW: Contrast and F-test

both of those contrasts are correct doug On 08/22/2013 10:51 AM, Jacobs H (NP) wrote: > Arrghh, again wrong email, sorry > > Thanks. I think I understand the rational behind it. > Just to be sure, would this be correct: > > For each group separately > 0 0 0 1 0 0 (group - cognition - educati

[Freesurfer] FW: FW: Contrast and F-test

Arrghh, again wrong email, sorry Thanks. I think I understand the rational behind it. Just to be sure, would this be correct: For each group separately 0 0 0 1 0 0 (group - cognition - education - cognition x education - age - ICV) For the F-test (same order) 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0

Re: [Freesurfer] FW: Contrast and F-test

you need to have all 3. If you want to examine the interaction, then you need a new contrast to test the interaction. Set all to 0 except for the interaction term doug On 08/22/2013 10:42 AM, Jacobs H (NP) wrote: > Dear Doug, > Thank you for the information. Sorry for not sending this to the li

[Freesurfer] FW: Contrast and F-test

Dear Doug, Thank you for the information. Sorry for not sending this to the list. Do you mean that I then have to include the three variables (covariate 1, covariate 2, product of these two) or only the product in the fsgd file? If I need to include all three of them, can you advise me on the con

Re: [Freesurfer] Contrast and F-test

If you want to test for an interaction between continuous variables, then you should create a new regressor by multiplying them together then test that regressor doug On 08/22/2013 08:09 AM, Jacobs H (NP) wrote: > Hi all, > > I my manuscript, I examined the association between cognition and cor

Re: [Freesurfer] [tracula] error running trac-all -prep

Hi Anastasia, I checked the dmri.bedpostx directory. Unless "nodif_brain", all files are there. Sincerely, Florian >>> Anastasia Yendiki 22.08.13 15.06 Uhr >>> Hi Florian - My guess is that everything ran fine and you don't need to change anything else. Check that all the output files were

Re: [Freesurfer] [tracula] error running trac-all -prep

Hi Florian - My guess is that everything ran fine and you don't need to change anything else. Check that all the output files were created in the dmri.bedpostX directory: http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html a.y On Thu, 22 Aug 2013, Borsodi Florian wrote: Hi A

Re: [Freesurfer] [tracula] error running trac-all -prep

Hi Anastasia, This Ubuntu-related error is a tricky one. I changed the first line in those files you told me and reran trac-all. All three steps of trac-all ran without any errrors. I checked the FA maps and the MNI registration and everything looks fine. After running trac-all -bedp, the st

[Freesurfer] Contrast and F-test

Hi all, I my manuscript, I examined the association between cognition and cortical thickness. I first did this in three groups separately and then ran a F-test. One of the reviewers, now wants me to examine the interaction between cognition and education (all continuous). Would this be the corr

[Freesurfer] mri_surf2surf to fsaverageX introduces offset

Dear Freesurfers, I tried to map a single subject surface to fsaverageX (for the sake of demonstration lets take fsaverage6). I did the following: mri_surf2surf --hemi lh --srcsubject $s --sval-xyz white --trgsubject fsaverage6 --tval-xyz --tval ./lh.white.ico6 This produces a surface that seems