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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Wighton, Paul PWIGHTON@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Shapiro, Noah Lorenz NLSHAPIRO@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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