Re: [Freesurfer] TRACULA Longitudinal can't find subject folder
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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA Longitudinal can't find subject folder
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 2016mri_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.gzmri_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 = FS1gOHzYgoG2UTR=10443.18, TE=0.00, TI=0.00, flip angle=0.00i_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 = FS1gOHzYgoG2Uif: _expression_ Syntax.#-/sw/freesurfer/5.3.0/bin/trac-preproc #-#@# Inter-subject registration (base template) Fri Feb 5 14:34:30 CET 2016cp /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/xfmscp: cannot stat ‘/data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/mni2anatorig.mat’: No such file or directorycp: cannot stat ‘/data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/anatorig2mni.mat’: No such file or directoryLinux 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/Linuxtrac-preproc exited with ERRORS at Fri Feb 5 14:34:30 CET 2016I 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. trac-all.error Description: Binary data trac-all.log Description: Binary data dmrirc.long Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA Longitudinal can't find subject folder
Hi Deniz - It seems that it finds the folders of the 2 time points, but not the folder of the longitudinal base template. This is the template that longitudinal recon-all creates in its 2nd processing step. In your case, it would be /data_august/Deniz/DTI_long/subjects/med_AhJa94 Does this exist? a.y On Thu, 4 Feb 2016, Gürsel, Deniz wrote: Dear Tracula Experts, I'm having trouble with longitudinal analysis using tracula. Just to try out, I am using one subject with 2 time points. I defined the parameters in dmrirc file as: set subjlist = (med_AhJa94_1 med_AhJa94_2) set baselist =(med_AhJa94 med_AhJa94) My subject folder which contains the longitudinal templates of reconstruction is located as "/data_august/Deniz/DTI_long/subjects/med_AhJa94_1.long.med_AhJa94" "/data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94" Tracula can't seem to find this subject folder, although I am providing the correct parameters for it. I get the error message when I ran trac-all -prep -c dmrirc.long : ERROR: cannot find /data_august/Deniz/DTI_long/subjects/med_AhJa94 I attached the trac-all.log and dmrirc files for your reference. Thank you very much. Best regards, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
