Just a guess: if you are using a Mac, the path for the directory should be something like

/Users/yourname/Desktop/ etc. instead of just /Desktop/ etc.

hope this helps, roberto

On Thu, Feb 18, 2010 at 10:15 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

The SUBJECTS_DIR is where you want the result of the freesurfer analysis to go. This is usually not /usr/local/freesurfer/subjects because you usually don't have write permissions. Try setting it to a place where you have some space, then run recon-all something like

recon-all -s yoursubject -i /Desktop/Allimages/MRIscan... and the full path till DICOM/dicomfile

the output will then be in $SUBJECTS_DIR/yoursubject

doug

Janani Dhinakaran wrote:

...

My data is on the desktop. The subjects directory is under usr/local/freesurfer/subjects. I tried setting desktop as SUBJECTS_DIR by using 'export SUBJECTS_DIR="/Desktop/Allimages/MRIscan... and the full path till DICOM" ' but apparently it didn't work because when I tried to run recon, it says  SUBJECTS_DIR /Desktop/Allimages/MRIscan/.../....DICOM does not exist

If I can't get SUBJECTS_DIR to change to Desktop path, how can I introduce my data into usr/local/freesurfer path? I notice Bert has everything in order. If I mkdir Mine in SUBJECTS_DIR and put my MRI files in there , will it work?

---

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

if 'jan' is your subject id your cmmdline needs to be:

recon-all -s jan -i <path to dicom file> -all

cheers Bruce On Fri, 19 Feb 2010, Janani Dhinakaran wrote:

Here are my attempts after exporting-

s0964091@CRIC-0012:~$ export SUBJECTS_DIR=~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/jan s0964091@CRIC-0012:~$ echo $SUBJECTS_DIR /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/jan s0964091@CRIC-0012:~$ echo $SUBJECTS_DIR /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/jan s0964091@CRIC-0012:~$ recon-all - jan -i /Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/jan ERROR: Flag - unrecognized.

• jan -i /Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/jan

Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC 2010 x86_64 GNU/Linux

recon-all exited with ERRORS at Fri Feb 19 13:18:33 GMT 2010

s0964091@CRIC-0012:~$ recon-all -s jan -i /Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/jan ERROR: cannot find /Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/jan Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC 2010 x86_64 GNU/Linux

recon-all exited with ERRORS at Fri Feb 19 13:21:28 GMT 2010

It doesn't seem to recognise the location even though I exported SUBJECTS_DIR to Desktop location. Jan

On 18 February 2010 21:15, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:

...

The SUBJECTS_DIR is where you want the result of the freesurfer analysis to go. This is usually not /usr/local/freesurfer/subjects because you usually don't have write permissions. Try setting it to a place where you have some space, then run recon-all something like

recon-all -s yoursubject -i /Desktop/Allimages/MRIscan... and the full path till DICOM/dicomfile

the output will then be in $SUBJECTS_DIR/yoursubject

doug

Janani Dhinakaran wrote:

...

My data is on the desktop. The subjects directory is under usr/local/freesurfer/subjects. I tried setting desktop as SUBJECTS_DIR by using 'export SUBJECTS_DIR="/Desktop/Allimages/MRIscan... and the full path till DICOM" ' but apparently it didn't work because when I tried to run recon, it says SUBJECTS_DIR /Desktop/Allimages/MRIscan/.../....DICOM does not exist

If I can't get SUBJECTS_DIR to change to Desktop path, how can I introduce my data into usr/local/freesurfer path? I notice Bert has everything in order. If I mkdir Mine in SUBJECTS_DIR and put my MRI files in there , will it work?

---

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html