Re: [Freesurfer] aparc+aseg.mgz for network analysis

I think you can use mri_binarize and set the match values as you like. Hope it can help. Best, Ismail > On Jul 21, 2016, at 2:13 PM, Jinsong Tang wrote: > > Hello freesurfers, > > I want to select the subcortical structures (thalamus, pallidum, caudate, > putamen,

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

ror having to do with the ascii header when unpacking skyra data on the mac, that might be it. Zeke, can you get Ismail a version of mri_convert appropriate for his OS? doug On 7/20/16 10:34 AM, Koubiyr, Ismail wrote: Hi Doug, I tried it on the cluster and it worked, which is weird because it was no

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

te: I used the same version, but I used it on linux. Do you have a linux box with FS installed that you can try it on? On 7/19/16 1:57 PM, Koubiyr, Ismail wrote: I used the same command line as you did. And when I check with mri_probedicom I can see the ASCII header. Here is the version of F

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

heck whether that file has an ascii header, run mri_probedicom --i MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 There should be a line like below ### ASCCONV BEGIN On 07/19/2016 01:16 PM, Koubiyr, Ismail wrote: Hi Doug, That’s weird because I can’t convert it using only mri_c

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

179441003292 output.nii.gz If I included -it dicom, the conversion did not have an error, but the output had only one slice. Since these are mosaics, they need the Siemens ascii header which is ignored with -it dicom. So ... don't use -it dicom On 07/19/2016 11:06 AM, Koubiyr, Ismail wr

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

p? > > On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote: >> The file has not been anonymized. >> >> Thanks, >> >> Ismail >> >>> On Jul 5, 2016, at 11:20 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> >>> wrote: >>> >

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

Hi, This is a repost. Would anyone have a solution to this problem ? Thanks for your help. Best, Ismail > On Jul 5, 2016, at 11:24 AM, Koubiyr, Ismail <ikoub...@bwh.harvard.edu> wrote: > > The file has not been anonymized. > > Thanks, > > Ismail > >> On

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

The file has not been anonymized. Thanks, Ismail > On Jul 5, 2016, at 11:20 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> > wrote: > > can you answer the question that it asks? > > On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote: >> Hi everyone, >> >

[Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

Hi everyone, I’m having some issues converting my DICOMs (DWI) into NIFTI using mri_convert. I looked for other topics with people having the same kind of problem but couldn’t find an answer. Each time I run mri_convert on my DICOMs I get the following error : WARNING: file

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

? ERROR: cannot unpack mosiacs without ASCII header Any idea what this could be ? Thanks, Ismail On Jul 4, 2016, at 3:15 PM, Koubiyr, Ismail <ikoub...@bwh.harvard.edu<mailto:ikoub...@bwh.harvard.edu>> wrote: It says 1 … I don’t understand why I get that knowing that when I open the ni

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

info on your > nifti, what is the number of frames that shows up? > > On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: > >> Hi Anastasia, >> >> This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. >> So this shouldn’t be the reas

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

> > It's trying to extract the 32nd frame of your nifti file, but from the error > message it looks like your nifti file doesn't have a 32nd frame. So either > the nifti file has too few volumes, or the bvecs/bvals have too many lines. > You'll have to figure that out. >

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

ds like the error has to do with the nifti volume, not the > bvecs/bvals. Can you send the log file from scripts/trac-all.log? > > Thanks, > a.y > > On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: > >> Hi Anastasia, >> Thank you for getting back to me. >> Here a

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

On Tue, 28 Jun 2016, Koubiyr, Ismail wrote: Hi everyone, I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error :

Re: [Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)

Hi Lars, I had the same problem. You can notice in your bvec file that there are some unusual blank spaces sometimes. Try to look at each space between two numbers and make sure it’s fine. You can also make sure about the number of entries by running wc -w on each of your bvec or bval file.

[Freesurfer] TRACULA problems

Hi everyone, It’s been two weeks that I’ve been facing some issues with Tracula. I hope you could help me with that. I run trac-all -prep -c on some DICOM files but I had the following error : WARNING: file

[Freesurfer] Tracula : ERROR: cannot unpack mosiacs without ASCII header

Hi everyone, I’m reposting my problem if someone could help me I would really appreciate it. I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c

[Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

Hi everyone, I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error : WARNING: file /My/path/to/dicom does not