These dof files are created by selxavg3-sess. If they are not there,
then that program must have failed in some way
On 6/29/2022 4:10 PM, Shapiro, Noah Lorenz wrote:
Hi Paul,
Thanks for your suggestion.
I examined all files within the /script directory from recon-all from
two subjects where one subject created a dof, and another did not
generate a dof. I used the vimdiff command to explore differences in
the files. There were significant differences in three of the log
files (from each subject); please be aware that I am new to
FreeSurfer, and I am not sure what these differences indicate. For
your convenience, I attached the files (.zip) and deidentified
subject-specific information with "Subject_with_dof" or
"Subject_with_no_dof".
What can I do to create the dof files to carry on with my analyses?
Any suggestions are very much appreciated.
Thank you in advance for your help.
Best wishes,
Noah
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Wighton, Paul
<pwigh...@mgh.harvard.edu>
*Sent:* 28 June 2022 11:10
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Problem with sxconcat-sess
Hi Noah,
I'm not super familiar with the functional stream, but it looks like
something has gone wrong during the first-level analysis for some of
your subjects.
Can you compare the log files in the ./scripts directory for a subject
that has the dof files vs a subject that doesn't and post any
differences you find?
-Paul
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Shapiro, Noah
Lorenz <nlshap...@mgh.harvard.edu>
*Sent:* Tuesday, June 28, 2022 8:35 AM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* [Freesurfer] Problem with sxconcat-sess
Hello,
I am trying to concatenate my functional data with the following
command (Ps: I am relatively new to FreeSurfer):
sxconcat-sess -sf functional_ID_jun22_allSubjects -analysis PCC_Bold_R
-contrast bilateral_isthmuscingulate_bold_config -o DMN_Right.
I get an error that says the dof file cannot be found for my 26 scans
in $SUBJECTS_DIR. However, running:
find . -name "dof"
The dof file was created for 12 scans. I used the same analysis
pipeline for all the scans. I searched the mailing list, and haven't
found anything that could help my problem. Any idea why the dof was
not created for all scans? How can I create the dof for the remaining
scans? Please let me know if you need further details. I am using
Freesurfer version 6.0.0.
Any help is very much appreciated.
Please find the terminal output below.
Best wishes,
Noah
actrumri[0]:RECONS$ echo $SUBJECTS_DIR
/autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS
actrumri[0]:RECONS$ isxconcat-sess -sf functional_ID_jun22_allSubjects
-analysis PCC_Bold_R -contrast bilateral_isthmuscingulate_bold_config
-o DMN_Right
DMN_Right/PCC_Bold_R/log/isxconcat.log
ERROR: cannot find
/autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS/RIB_668_018_3_recon.long.RIB_668_018/bold/PCC_Bold_R/dof
actrumri[0]:RECONS$ find . -name "dof"
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_L/dof
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_V/dof
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_R/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_L/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_V/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_R/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_L/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_V/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_R/dof
./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_L/dof
./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_V/dof
./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_R/dof
actrumri[0]:RECONS$ isxconcat-sess -sf functional_ID_jun22_allSubjects
-analysis PCC_Bold_L -contrast bilateral_isthmuscingulate_bold_config
-o DMN_Left
DMN_Left/PCC_Bold_L/log/isxconcat.log
ERROR: cannot find
/autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS/RIB_668_018_3_recon.long.RIB_668_018/bold/PCC_Bold_L/dof
actrumri[0]:RECONS$ find . -name "dof"
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_L/dof
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_V/dof
./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_R/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_L/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_V/dof
./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_R/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_L/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_V/dof
./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_R/dof
./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_L/dof
./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_V/dof
./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_R/dof
actrumri[0]:RECONS$
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