Can you upload the functional volume to ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Let me know when it is there and what the file name is

On 4/16/19 5:55 PM, Mcnorgan, Christopher wrote:

External Email - Use Caution

Hi Doug,

For some reason I’m having a problem replying to this list with my reply to your reply. To recap: some of my functional runs are missing the mcprextreg file, and so the GLM with the motion correction parameters is failing.

You had asked whether a mc-subjectname-bold.log file exists for these data. These log files do exist, and I’ve tried a couple times to send the log files (1MB attachment rejected). I’m including a google drive link to one of the log files in the hopes that your offer still stands to get to the bottom of why these files are reliably not being created for some runs, while created for other runs collected during the same session: https://drive.google.com/open?id=17GLikK1mzY5uL52TyqlGK0Sa5N5Fy1KY

We’ve been acutely aware of how many data frames are in each 4D volume because the scanner has been incorrectly writing that all volumes are 256 frames, though our self-paced experiment terminates earlier to that. We accidentally found the fix to be to open up the header using fsledithd, which then zero-pads the missing data frames until we have 256. However this is the case for all runs, so that doesn’t explain why only some runs are failing.

Thanks, Chris

/**********************************************

• Chris McNorgan
• Assistant Professor
• Department of Psychology
• University at Buffalo,
• The State University of New York
• http://ccnlab.buffalo.edu/
• Office: 716.645.0236
• Lab: 716.645.0222

**********************************************/

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer