26 Aug
2020
26 Aug
'20
9:07 a.m.
That file was apparently not created when running mri_glmfit-sim, but the log files did not show an error
On 8/25/2020 12:18 PM, Diógenes Diego wrote:
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What is the reason for this message?
ERROR: could not open lh.volume.example.10.glmd/csd/all.cache.th13.pos-CONTROLE-PK.csd
Thanks
Diogenes Bispo
Em 25 de ago de 2020, à(s) 12:22, Douglas N. Greve dgreve@mgh.harvard.edu escreveu:
It does not look like any of those have errors?
On 8/25/2020 8:56 AM, Diógenes Bispo wrote:
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Here follows the screen capture for the --debug option within the commands.
Really appreciate all the help.
Sincerely.
Diógenes Bispo diogenesdiego@gmail.com mailto:diogenesdiego@gmail.com
Em dom., 23 de ago. de 2020 às 12:41, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> escreveu:
There was nothing attached, but the summary is probably not too helpful. Can you run it again with --debug as the first option. Capture the terminal output in a file and send it in. On 8/22/2020 5:04 PM, Diógenes Bispo wrote:External Email - Use Caution Hi Freesurfer Community, I'm using Freesurfer for the volumetric analysis of Parkinson's patients in comparison with a control group. While trying to execute it for a sample of 6 patients (3 from each group), I got one error during the mri_glmfit-sim. I did execute the mris_preproc and mri_glmfit before it. These are all the steps: First created the FSGD and contrast folders. I did copy the fsaverage to the local folder. All the comands were executed under the local folder within the structure: drwxr-xr-x 2 vinicius vinicius 4096 ago 3 09:53 Contrasts drwxrwxrwx 10 vinicius vinicius 4096 jun 15 10:08 DPV1_ACM1604 drwxrwxrwx 10 vinicius vinicius 4096 jun 14 22:26 DPV1_APA1311 drwxrwxrwx 10 vinicius vinicius 4096 jun 14 22:28 DPV1_CEM1702 -rw-r--r-- 1 vinicius vinicius 210 ago 3 10:12 example.fsgd drwxrwxrwx 8 vinicius vinicius 4096 nov 13 2015 fsaverage drwxr-xr-x 2 vinicius vinicius 4096 ago 3 10:14 FSGD drwxrwxrwx 10 vinicius vinicius 4096 jun 14 22:31 GCV1_FCB0701 drwxrwxrwx 10 vinicius vinicius 4096 jun 14 22:34 GCV1_JCC2509 drwxrwxrwx 10 vinicius vinicius 4096 jun 14 22:36 GCV1_JCC2902 FSGD file used was the example.fsgd and its contents are: GroupDescriptorFile 1 Title example Class CONTROLE Class PK Input GCV1_FCB0701 CONTROLE Input GCV1_JCC2509 CONTROLE Input GCV1_JCC2902 CONTROLE Input DPV1_ACM1604 PK Input DPV1_APA1311 PK Input DPV1_CEM1702 PK Created the Contrasts files CONTROLE-PK.mtx, and it's contents: 1 -1 PK-CONTROLE.mtx, and it's contents: -1 1 Used the local folder as SUBJECTS_DIR: export SUBJECTS_DIR=$('pwd') export LC_NUMERIC="en_US.UTF-8" Started with the mris_preproc: mris_preproc --fsgd /home/vinicius/fsteste/example.fsgd --cache-in volume.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.volume.example.10.mgh mris_preproc --fsgd /home/vinicius/fsteste/example.fsgd --cache-in volume.fwhm10.fsaverage --target fsaverage --hemi lh --out rh.volume.example.10.mgh mris_preproc --fsgd /home/vinicius/fsteste/example.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.thickness.example.10.mgh mris_preproc --fsgd /home/vinicius/fsteste/example.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi rh --out rh.thickness.example.10.mgh All the outputs were attached in the file mris_preproc.zip After that I did execute the mri_glmfit: mri_glmfit --y lh.volume.example.10.mgh --fsgd /home/vinicius/fsteste/example.fsgd --C /home/vinicius/fsteste/Contrasts/CONTROLE-PK.mtx --C /home/vinicius/fsteste/Contrasts/PK-CONTROLE.mtx --surf fsaverage lh --cortex --glmdir lh.volume.example.10.glmd mri_glmfit --y rh.volume.example.10.mgh --fsgd /home/vinicius/fsteste/example.fsgd --C /home/vinicius/fsteste/Contrasts/CONTROLE-PK.mtx --C /home/vinicius/fsteste/Contrasts/PK-CONTROLE.mtx --surf fsaverage rh --cortex --glmdir rh.volume.example.10.glmd mri_glmfit --y lh.thickness.example.10.mgh --fsgd /home/vinicius/fsteste/example.fsgd --C /home/vinicius/fsteste/Contrasts/CONTROLE-PK.mtx --C /home/vinicius/fsteste/Contrasts/PK-CONTROLE.mtx --surf fsaverage lh --cortex --glmdir lh.thickness.example.10.glmd mri_glmfit --y rh.thickness.example.10.mgh --fsgd /home/vinicius/fsteste/example.fsgd --C /home/vinicius/fsteste/Contrasts/CONTROLE-PK.mtx --C /home/vinicius/fsteste/Contrasts/PK-CONTROLE.mtx --surf fsaverage rh --cortex --glmdir rh.thickness.example.10.glmd All the outputs were attached in the file mris_preproc.zip When I try to execute the mri_glmfit-sim with the command: mri_glmfit-sim --glmdir lh.volume.example.10.glmd --cache 1.3 pos --cwp 0.05 --2spaces I get the following error: ERROR: could not open lh.volume.example.10.glmd/csd/all.cache.th13.pos-CONTROLE-PK.csd The folder lh.volume.example.10.glmd/csd was not created. All subjects were processed using version 7 without qcache and then executed the qcache separately later on. Attached the entire output of the command: output_lh.volume.example.10.glmd.txt Also attached the summary of the lh.volume.example.10.glmd cache.th13.pos.sig.cluster.summary System: Ubuntu LTS 18.04. Please, help me to fix this error or help me to figure out what I'm doing wrong. Thank you! Diógenes Bispo diogenesdiego@gmail.com <mailto:diogenesdiego@gmail.com> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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