External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to do group analysis for cortical thickness map using Qdec GUI. We've already have recon-all files that were made by “recon-all –s subjid –i subjid.nii –all” on other Linux OS (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0)
Firstly, I try to run command “recon-all –s subject –qcache” for each subject floders. However, the program stopped with error 1 minutes after starting. Last line of recon-all.log showed as follows.
#@# Qdec Cache preproc lh white.K fsaverage Thu Dec 20 12:03:25 EST 2018 /Users/emitakahashi/freesurfer/subjects/ASD001/surf \n mris_preproc --s ASD001 --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh \n nsubjects = 1 ERROR: cannot find /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.white.K Darwin emis-mbp.tch.harvard.edu 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64
I've searched the list but I can find no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: Free Surfer 6.0 2) Platform: macOS Mojave (64b Intel) 3) recon-all.log: see attached
Tadashi Shiohama
Does that file exist? If not, check to see whether that subject finished or whether there was an error
On 12/20/18 2:37 PM, 塩浜 直 wrote:
External Email - Use CautionHello FreeSurfer Developers,
I'm attempting to do group analysis for cortical thickness map using Qdec GUI. We've already have recon-all files that were made by “recon-all –s subjid –i subjid.nii –all” on other Linux OS (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0)
Firstly, I try to run command “recon-all –s subject –qcache” for each subject floders. However, the program stopped with error 1 minutes after starting. Last line of recon-all.log showed as follows.
#@# Qdec Cache preproc lh white.K fsaverage Thu Dec 20 12:03:25 EST 2018 /Users/emitakahashi/freesurfer/subjects/ASD001/surf \n mris_preproc --s ASD001 --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh \n nsubjects = 1 ERROR: cannot find /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.white.K Darwin emis-mbp.tch.harvard.edu 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64
I've searched the list but I can find no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: Free Surfer 6.0 2) Platform: macOS Mojave (64b Intel) 3) recon-all.log: see attached
Tadashi Shiohama
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Dr. Greve,
I found out the reason why it does not work. That was because the subjects' folder does not include lh white.K. Thank you so much!
Tadashi Shiohama
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Friday, January 4, 2019 4:21 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -qcache error
Does that file exist? If not, check to see whether that subject finished or whether there was an error
On 12/20/18 2:37 PM, 塩浜 直 wrote:
External Email - Use CautionHello FreeSurfer Developers,
I'm attempting to do group analysis for cortical thickness map using Qdec GUI. We've already have recon-all files that were made by “recon-all –s subjid –i subjid.nii –all” on other Linux OS (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0)
Firstly, I try to run command “recon-all –s subject –qcache” for each subject floders. However, the program stopped with error 1 minutes after starting. Last line of recon-all.log showed as follows.
#@# Qdec Cache preproc lh white.K fsaverage Thu Dec 20 12:03:25 EST 2018 /Users/emitakahashi/freesurfer/subjects/ASD001/surf \n mris_preproc --s ASD001 --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh \n nsubjects = 1 ERROR: cannot find /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.white.K Darwin emis-mbp.tch.harvard.edu 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64
I've searched the list but I can find no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use.
- FreeSurfer version: Free Surfer 6.0
- Platform: macOS Mojave (64b Intel)
- recon-all.log: see attached
Tadashi Shiohama
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@nmr.mgh.harvard.edu
-
Greve, Douglas N.,Ph.D. -
Tadashi Shiohama -
塩浜 直