Hi Danny
you need to specify a subject name/id with -s <id>
cheers Bruce On Wed, 22 Nov 2017, Danny Deng wrote:
Dear FS developers, I have problem as follow when I tried file input/output (original images can not be identified)
Xues-MacBook-Air:00000001 DannyDeng$ recon-all -i im_0001.dcm ERROR: must specify a subject id Xues-MacBook-Air:00000001 DannyDeng$ recon-all -i IM_0001.dcm -s anon mkdir: /Applications/freesurfer/subjects/anon: Permission denied mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied cp: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such file or directory cat: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c /Applications/freesurfer/subjects/anon/scripts/patchdir.txt: No such file or directory. Xues-MacBook-Air:00000001 DannyDeng$ recon-all -i IM_0001.dcm -s anon mkdir: /Applications/freesurfer/subjects/anon: Permission denied mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied cp: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such file or directory cat: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c /Applications/freesurfer/subjects/anon/scripts/patchdir.txt: No such file or directory. Xues-MacBook-Air:00000001 DannyDeng$
Please help.
Thanks.
Best Regards,Danny Deng
On Nov 22, 2017, at 1:33 AM, Hwee Ling Lee <hweeling.lee@gmail.com> wrote:Dear Bruce, Thanks for your reply. I checked the folder and did not find the file that was requested.
What I have in the average folder that has 'RB*.gca' are 'RB_all_2016-05-10.vc700.gca' and 'RB_all_withskull_2016-05-10.vc700.gca'. The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'.
Cheers, Hweeling
On Nov 21, 2017 18:05, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote: Hi Hweeling
what is FREESURFER_HOME set to in the environment? Does that file exist? It is a standard part of our distribution cheers Bruce On Tue, 21 Nov 2017, Hwee Ling Lee wrote: Dear all, I have T1 images collected from the 7T MRI scanner. I downloaded the most recent freesurfer software, and followed all instructions to install the software before using it. I would like to segment the T1 data using its high resolution image, and also to segment the hippocampal subfields. For command, I use this: recon-all -all -s <subject name> -hires -i <subject dicom T1 image frame 1 location> However, I get an error message: cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca I'm not sure what I did wrong. Also, how can I combine high resolution segmentation and hippocampal subfields segmentation? Could someone please help? Thanks. Best regards, Hweeling The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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