Hi again Deniz - This may be confusing but with longitudinal TRACULA there are separate trac-all.log files in each time point's directory and in the within-subject template's directory. The former are for things that are run independently for each time point (mainly pre-processing) and the latter for things that are run jointly for all time points (like tractography).

I suspect that the first error probably occured earlier, and it can be found in the log file of one of the time points.

In your configuration file, use bvecfile if you're using a single gradient table for all data sets and bveclist if you have a different one for each time point.

Hope this helps,

a.y

On Fri, 5 Feb 2016, Deniz Gursel wrote:

Dear Anastasia,

Thank you very much for your fast solution. Indeed, I was missing the related folders, I haven’t run the recon-all myself and I copied only the final folder and not the whole as a mistake. Now, I passed that error and got stuck with a new one.

In the inter-subject registration step, I get the error:

#@# Image corrections Fri Feb 5 14:34:25 CET 2016 mri_convert /data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94/dwi.nii /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_2.long.med_AhJa94/dmri/dwi_orig.nii.gz mri_convert /data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94/dwi.nii /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_2.long.med_AhJa94/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94/dwi.nii... crypt_gkey = FS1gOHzYgoG2U TR=10443.18, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998789, 0.0474208, 0.0131247) j_ras = (0.0473438, 0.99886, -0.00611764) k_ras = (0.0133998, 0.00548885, 0.999895) writing to /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_2.long.med_AhJa94/dmri/dwi_orig.nii.gz... crypt_gkey = FS1gOHzYgoG2U if: Expression Syntax. #------------------------------------- /sw/freesurfer/5.3.0/bin/trac-preproc #------------------------------------- #@# Inter-subject registration (base template) Fri Feb 5 14:34:30 CET 2016 cp /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/mni2anatorig.mat /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/anatorig2mni.mat /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94/dmri/xfms cp: cannot stat ‘/data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/mni2anatorig.mat’: No such file or directory cp: cannot stat ‘/data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/anatorig2mni.mat’: No such file or directory Linux slow.mri.tu-muenchen.de 3.7.10-1.40-desktop #1 SMP PREEMPT Thu Jul 10 11:22:12 UTC 2014 (9b06319) x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Feb 5 14:34:30 CET 2016

I am attaching the trac_all.log, trac_all.error and dmrirc for you. Also, before the error, at the image correction step, there is “if: expression syntax” message which I couldn’t figure out why it happens. I looked it up and seems like some Unix error. I encountered it many times, when I was running another cross-sectional study and sometimes it went away magically.

Thank you very much for your time and help.