External Email - Use Caution
I followed your given link and ran sudo -E fs_update and came up with the following error just wanted to know is this error related to SIP or is it a some other issue.
PILEPSY:subjects eoilepsyosirixadmin$ sudo -E fs_update
Build is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Running this will update some of your freesurfer binaries.
Shall I proceed? [y/n/Abort]: y
rsync -zbrlv --progress --suffix=.1571729614_bak rsync:// surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/* /Applications/freesurfer
receiving incremental file list
rsync: change_dir "/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" (in pub) failed: No such file or directory (2)
sent 8 bytes received 163 bytes 31.09 bytes/sec
total size is 0 speedup is 0.00 rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1679) [Receiver=3.1.3]
Thanks and Regards Nayan Wadhwani
On Mon, Oct 21, 2019 at 11:46 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
The error message in your log file ("dyld: Symbol not found...") has been addressed here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61247.html
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of nayan wadhwani < nayanw775@gmail.com> *Sent:* Tuesday, October 22, 2019 2:32 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] trac-all error
External Email - Use CautionI have attached the log-file from the trac-all command Thanks and Regards Nayan Wadhwani
On Mon, Oct 21, 2019 at 10:26 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Please attach your log file from scripts/trac-all.log.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of nayan wadhwani < nayanw775@gmail.com> *Sent:* Tuesday, October 22, 2019 1:13 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] trac-all error
External Email - Use CautionHello Freesurfer,
I did changes asked by you but still error persists. While i am using dicom images why it is asking for NIFTI format. I checked the lib folder also and checked and all the files mention above are there in the folder. Do i need to check something else.
Sent from my iPhone
On 22-Oct-2019, at 8:01 AM, Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
Hi Nayan - Try using /Applications instead of $Applications everywhere. Also, the config file seems to be in rich text format - not sure how that'll work. Try converting it to plain text (if you use mac, from the Format menu of the text editor).
Best, Anastasia.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of nayan wadhwani < nayanw775@gmail.com> *Sent:* Saturday, October 19, 2019 1:36 AM *To:* Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] trac-all error
External Email - Use CautionHello Freesurfer,
After running recon all script which completed successfully, I ran trac-all command which exited with error and tried running it with dicom files.
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ___emutls_get_address
Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
Expected in: /usr/lib/libSystem.B.dylib
Abort
ERROR: input file must be in NIfTI format
Darwin EPILEPSY 16.7.0 Darwin Kernel Version 16.7.0: Mon Nov 13 21:56:25 PST 2017; root:xnu-3789.72.11~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Fri Oct 18 22:13:02 PDT 2019
And please help me the correct config the one I created, I am attaching it below to try it with .nii files Thanks and Regards Nayan Wadhwani
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