To all
Has anyone had any experience using an external drive with freesurfer (under LINUX)?
I am trying to use a FAT32 drive with Freesurfer (I also use this drive with XP) and I keep running into the following error:
"First T1 image: /mnt/usb/afnidata/subjects/bert/mri/T1/COR-001 not found"
However, when I check, the file is there but is listed in lower-case (i.e., "cor-001"). I cannot rename the file to upper-case - the file already exists...
Is Freesurfer case-sensitive and if so, is there a way to tell it to look for lower-case filenames?
Thanks
Andy
we use fopen, so if the instantiation of it on an os is case sensitive (as in linux) then we are as well. You might try converting the COR volume to something else (e.g. afni) and name it all lower case. It's only in this instance that the names of the files are hardcoded. e.g.:
mri_convert $SUBJECTS_DIR/$subject/mri/orig $SUBJECTS_DIR/mri/orig.brik
cheers, Bruce
On Mon, 6 Jun 2005, Andrew H Bell wrote:
To all
Has anyone had any experience using an external drive with freesurfer (under LINUX)?
I am trying to use a FAT32 drive with Freesurfer (I also use this drive with XP) and I keep running into the following error:
"First T1 image: /mnt/usb/afnidata/subjects/bert/mri/T1/COR-001 not found"
However, when I check, the file is there but is listed in lower-case (i.e., "cor-001"). I cannot rename the file to upper-case - the file already exists...
Is Freesurfer case-sensitive and if so, is there a way to tell it to look for lower-case filenames?
Thanks
Andy
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On Monday 06 June 2005 17:41, Andrew H Bell wrote:
However, when I check, the file is there but is listed in lower-case (i.e., "cor-001"). I cannot rename the file to upper-case - the file already exists...
You might try renaming the files to upper case in this manner:
(In a Windows command prompt)
C:> cd <data\directory> C:\data\directory> move T1 TT1 C:\data\directory> mkdir T1 C:\data\directory> copy TT1\cor* T1\COR*
and you should be all set. Repeat for other directories.
In Linux, you might do the following (*):
~> cd /data/directory /data/directory> mv T1 TT1 /data/directory> mkdir T1 /data/directory> cd TT1 /data/directory> /bin/ls -1 COR* | awk -F- '{printf("cp cor-%s ../T1/COR-%s\n", $2, $2)}' | sh -v
(The above command should all be on one line).
--R
(*) Note that there are probably many different ways to do this in Linux.
freesurfer@nmr.mgh.harvard.edu