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
diogenesdi...@gmail.com <mailto:diogenesdi...@gmail.com>
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