Dear Sir / madam,
I'm a last year student of Medical Imaging (from Hoge school Universiteit Brussel, HUB). In January i'm defending my thesis. My subject is MRI and Alzheimer's disease. With volumetry I want to show that the Hippocampi have a smaller volume then normal patients.
I used the program: SPM, VBM and IBASPM previous year, but I got weird results from those software. My supervisors said that it's probably the best to use a new software, so i'm trying to use Freesurfer.
I'm not used to programming with Linux (Xbuntu), so it's a bit difficult for me personally. Also the physicist (who i colaborate with) isn't used to programming.
This is my problem: When i open Virtualbox (installed with freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full) I go to
file-system -> usr -> local -> freesurfer -> subjects (the map where also the subject"Bert" is in it). In the subject-folder is paste a folder with only T1-Dicom images.
After i copied & pasted the DICOM-files in the subjects folder, i go to the "terminal". There I type: "tcsh" to setup freesurfer (I read it on the Freesurfer wiki site).
After that I type:
recon-all -s <new folder where the new made files are putted in> \ -i $SUBJECTS_DIR/<name of the folder where my DICOM-files are in (here i made an archive of the DICOM-files, extented with .mgz) > \ -autorecon1
When i hit Enter, i get a message that says: "tcsh v6.17.06 has an exit code bug! Please update tcsh!"
There is also a new folder created, with some subfolders (BEM, label, scripts , MRI ,etc.). But there is nothing to see in those folders.
My question is how can I update tcsh so I can do the recon-all procedure?
Hopefully you can help me,
Thank you in advance, Kind regards,
Philippe Blaes (3rd year Medical Imaging)
Hi Philippe, See link below regarding the error you are getting, although recon-all is probably failing because you need to pass not only the path but one dicom file which is part of the T1-weighted scan. If you run the command below in the directory where you copied the dicom files, you will get an unpack.log as output listing each run and the first dicom in each series. Pick out the run you want to process in Freesurfer and include the associated dicom file at the end of the argument passed with the -i flag.
unpacksdcmdir -scanonly scan.log -src . -targ .
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28978.html
On Mon, 21 Oct 2013, Philippe Blaes wrote:
Dear Sir / madam,
I'm a last year student of Medical Imaging (from Hoge school Universiteit Brussel, HUB). In January i'm defending my thesis. My subject is MRI and Alzheimer's disease. With volumetry I want to show that the Hippocampi have a smaller volume then normal patients. I used the program: SPM, VBM and IBASPM previous year, but I got weird results from those software. My supervisors said that it's probably the best to use a new software, so i'm trying to use Freesurfer. I'm not used to programming with Linux (Xbuntu), so it's a bit difficult for me personally. Also the physicist (who i colaborate with) isn't used to programming.
This is my problem: When i open Virtualbox (installed with freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full) I go to file-system -> usr -> local -> freesurfer -> subjects (the map where also the subject"Bert" is in it). In the subject-folder is paste a folder with only T1-Dicom images.
After i copied & pasted the DICOM-files in the subjects folder, i go to the "terminal". There I type: "tcsh" to setup freesurfer (I read it on the Freesurfer wiki site). After that I type:
recon-all -s <new folder where the new made files are putted in> \ -i $SUBJECTS_DIR/<name of the folder where my DICOM-files are in (here i made an archive of the DICOM-files, extented with .mgz) > \ -autorecon1
When i hit Enter, i get a message that says: "tcsh v6.17.06 has an exit code bug! Please update tcsh!"
There is also a new folder created, with some subfolders (BEM, label, scripts , MRI ,etc.). But there is nothing to see in those folders.
My question is how can I update tcsh so I can do the recon-all procedure?
Hopefully you can help me, Thank you in advance, Kind regards, Philippe Blaes (3rd year Medical Imaging)
freesurfer@nmr.mgh.harvard.edu
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Louis Nicholas Vinke -
Philippe Blaes