Hi Katica
after you move the dicoms you have to run recon-all. Something like:
recon-all \ -sd /usr/local/freesurfer/subjects2 \ -s <subject id that you pick> \ -i <path to 1 file in the correct dicom series> \ -all
this will create the directory
/usr/local/freesurfer/subjects2/<subject id that you pick>
and populate it with the analysis results average 10-14 hours or so
cheers Bruce
On Tue, 3 Sep 2013, Boric, Katica A. wrote:
Hi Bruce! So, before my subject folder was in a shared folder with the VM and my PC
(mnt/hgfs/Linux_Share/subjects)
After the recon with errors (see first emails) I was advised to set the
subject folder (which I understand is where the dicoms are stored, but I might be mistaken) locally to the same freesurfer home (usr/local/freesurfer/). So I created a new folder called subjects2 (usr/local/freesurfer/subjects2) and moved a folder with dicoms of one patien that was in the Shared folder, to this new folder. After that, I did: setenv SUBJECTS_DIR /usr/local/freesurfer/subjects2
and I didn't get any "message" Is this specific enough? Sorry, I am really new to freesurfer! Thank you very much, Katica ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, September 03, 2013 3:05 PM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error in MRI processing
Hi Katicia
can you be more detailed about what you did? What command did you issue after you moved the dicoms? Where did you move them to? In general you shouldn't need to move the dicoms. Bruce On Tue, 3 Sep 2013, Boric, Katica A. wrote:
Hi Bruce! So I created a new subject folder in the same local system of freesurfer. Since there already was a folder named subjects in usr/local/freesurfer I named it subjects 2: /usr/local/freesufer/subjects2
I moved the dicoms into this new folder. Then I did setenv SUBJECTS_DIR /usr/local/freesurfer/subjects2 and nothing happened. Am I doing something wrong?
Thanks, Katica
From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, September 03, 2013 12:08 PM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error in MRI processing
oh, then
setenv SUBJECTS_DIR new_path
On Tue, 3 Sep 2013, Boric, Katica A. wrote:
Thanks Bruce! So, I just move the SUBJECT_DIR folder and then setenv? I do want to set the subject directory to a new path Thanks again, Katica ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Tuesday, September 03, 2013 12:03 PM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error in MRI processing
setenv FREESURFER_HOME /usr/local/freesurfer
On Tue, 3 Sep 2013, Boric, Katica A. wrote:
Hi everyone! I wrote you last Friday regarding an error at the last moment of the MRI processing (see e-mails below) Zeke: thanks so much for the advice, I will move the SUBJECT_DIR to the same folder system as $FREESURFER_HOME. Could someone please show me how to set the directory with a tcsh shell? The path to the freesurfer home is: usr/local/freesurfer
Thank you very much, Katica
From: Z K [zkaufman@nmr.mgh.harvard.edu] Sent: Friday, August 30, 2013 12:41 PM To: Boric, Katica A. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error in MRI processing
Katica,
The file system in the physical computer is NTFS. But it looks like the SUBJECTS_DIR is on a mounted filesystem. And your on a virtual machine. Unfortunately there's lots of possibilities here for some type of incompatibility with symbolic links.
Would it be possible for you to set the SUBJECTS_DIR to be on the same file system as $FREESURFER_HOME (locally) in order to avoid any potential conflicts?
-Zeke
On 08/30/2013 11:54 AM, Boric, Katica A. wrote:
Hi Doug! I am using free surfer on a VM. The file system in the physical computer is NTFS. Thanks, Katica ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, August 30, 2013 11:46 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error in MRI processing
I think this error
ln: failed to create symbolic link `./fsaverage': Operation not supported
is a problem with your file system. Are you using a FAT file system?On 08/30/2013 11:41 AM, Boric, Katica A. wrote:
Hi Bruce this comes out from ls -ald $FREESURFER_HOME/subjects/fsaverage
drwxr-xr-x. 7 root root 4096 Oct 23 2012 /usr/local/freesurfer/subjects/fsaverage ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, August 30, 2013 11:15 AM To: Boric, Katica A. Subject: Re: [Freesurfer] error in MRI processing
how about:
On Fri, 30 Aug 2013, Boric, Katica A. wrote:
> This comes out: > drwxrwxrwx. 1 root root 0 Aug 29 11:10 /mnt/hgfs/Linux_Share/subjects > ________________________________________ > From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] > Sent: Friday, August 30, 2013 11:11 AM > To: Boric, Katica A. > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] error in MRI processing > > that probably means you don't have write access to the subject directory. > Can you run: > > ls -ald /mnt/hgfs/Linux_Share/subjects > > On Fri, 30 Aug 2013, Boric, Katica A. > wrote: > >> It says: >> $ ln -s /usr/local/freesurfer/subjects/fsaverage >> ln: failed to create symbolic link `./fsaverage': Operation not supported >> >> ________________________________________ >> From: freesurfer-bounces@nmr.mgh.harvard.edu >> [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fischl@nmr.mgh.harvard.edu] >> Sent: Friday, August 30, 2013 11:04 AM >> To: Boric, Katica A. >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] error in MRI processing >> >> can you run: >> >> cd /mnt/hgfs/Linux_Share/subjects >> ln -s /usr/local/freesurfer/subjects/fsaverage >> >> and tell us what it says? >> Bruce >> On Fri, 30 Aug 2013, Boric, >> Katica A. >> wrote: >> >>> Hi Bruce! >>> Thanks for your fast response. >>> /usr/local/freesurfer/subjects/fsaverage does exists! >>> >>> Thanks again, >>> Katica >>> ________________________________________ >>> From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] >>> Sent: Friday, August 30, 2013 10:51 AM >>> To: Boric, Katica A. >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] error in MRI processing >>> >>> Hi Katica >>> >>> does /usr/local/freesurfer/subjects/fsaverage exist? Do you have write >>> access to /mnt/hgfs/Linux_Share/subjects? >>> >>> cheers >>> Bruce >>> >>> On Fri, 30 Aug 2013, Boric, Katica A. wrote: >>> >>>> Hi everyone! >>>> I am new to freesurfer, and I was processing and MRI using "recon-all >>>> -autorecon1 -autorecon2 -autorecon3" command and I have a message that >> the >>>> processing was exited with ERRORS. When checking the recon-all. log it >>>> appears that these are the error (highlighted in yellow): >>>> >>>> #@# BA Labels lh Thu Aug 29 22:14:42 PDT 2013 >>>> INFO: fsaverage subject does not exist in SUBJECTS_DIR >>>> INFO: Creating symlink to fsaverage subject... >>>> >>>> cd /mnt/hgfs/Linux_Share/subjects; ln -s >>>> /usr/local/freesurfer/subjects/fsaverage; cd - >>>> >>>> ln: failed to create symbolic link `./fsaverage': Operation not supported >>>> >>>> mri_label2label --srcsubject fsaverage --srclabel >>>> /mnt/hgfs/Linux_Share/subjects/fsaverage/label/lh.BA1.label --trgsubject >>>> MGH013_SurferOutput --trglabel ./lh.BA1.label --hemi lh --regmethod >> surface >>>> No such file or directory >>>> mri_label2label: could not open label file >>>> /mnt/hgfs/Linux_Share/subjects/fsaverage/label/lh.BA1.label >>>> >>>> srclabel = /mnt/hgfs/Linux_Share/subjects/fsaverage/label/lh.BA1.label >>>> srcsubject = fsaverage >>>> trgsubject = MGH013_SurferOutput >>>> trglabel = ./lh.BA1.label >>>> regmethod = surface >>>> >>>> srchemi = lh >>>> trghemi = lh >>>> trgsurface = white >>>> srcsurfreg = sphere.reg >>>> trgsurfreg = sphere.reg >>>> usehash = 1 >>>> Use ProjAbs = 0, 0 >>>> Use ProjFrac = 0, 0 >>>> DoPaint 0 >>>> >>>> SUBJECTS_DIR /mnt/hgfs/Linux_Share/subjects >>>> FREESURFER_HOME /usr/local/freesurfer >>>> Loading source label. >>>> Invalid argument >>>> ERROR reading /mnt/hgfs/Linux_Share/subjects/fsaverage/label/lh.BA1.label >>>> Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 >> 20:57:42 >>>> UTC 2013 x86_64 x86_64 x86_64 GNU/Linux >>>> >>>> recon-all -s MGH013_SurferOutput exited with ERRORS at Thu Aug 29 >> 22:14:43 >>>> PDT 2013 >>>> >>>> If any of you could give us any advice on how to fix this we would really >>>> appreciate it! >>>> Thank you very much, >>>> >>>> Cheers, >>>> Katica >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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