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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