Hi Bruce,
Sure, please see highlighted below part of screen output showing the error. Since I ran the command within a screen sesison I have saved executed screen session to a log file. Find attached log file with output of entire run. Please let me know if any other files are required and if attached log file could be interpreted. Read individual LTAs Writing LTA to file ped1_base_to_ped1_0.lta... mri_concatenate_lta successful. mri_concatenate_lta -invert1 ped1_1_to_ped1_base.lta identity.nofile ped1_base_to_ped1_1.lta invert the first LTA before applying it Read individual LTAs Writing LTA to file ped1_base_to_ped1_1.lta... mri_concatenate_lta successful. mri_concatenate_lta -invert1 ped1_2_to_ped1_base.lta identity.nofile ped1_base_to_ped1_2.lta invert the first LTA before applying it Read individual LTAs Writing LTA to file ped1_base_to_ped1_2.lta... mri_concatenate_lta successful. mri_concatenate_lta -invert1 ped1_3_to_ped1_base.lta identity.nofile ped1_base_to_ped1_3.lta invert the first LTA before applying it Read individual LTAs Writing LTA to file ped1_base_to_ped1_3.lta... mri_concatenate_lta successful. mri_concatenate_lta -invert1 ped1_4_to_ped1_base.lta identity.nofile ped1_base_to_ped1_4.lta invert the first LTA before applying it Read individual LTAs Writing LTA to file ped1_base_to_ped1_4.lta... mri_concatenate_lta successful. #-------------------------------------------- #@# MotionCor Wed Jul 26 14:04:13 EDT 2017 mri_add_xform_to_header -c /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/transforms/talairach.xfm /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/orig.mgz /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Wed Jul 26 14:04:14 EDT 2017 /shared_data2/sneha/MSKCC_Processed/ped1_base/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux gizmo 4.4.0-78-generic #99-Ubuntu SMP Thu Apr 27 15:29:09 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ped1_base exited with ERRORS at Wed Jul 26 14:04:17 EDT 2017 For more details, see the log file /shared_data2/sneha/MSKCC_Processed/ped1_base/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thanks, Sneha ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu> Sent: Monday, August 7, 2017 2:02:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical thickness map for a pediatric case Hi Sneha can you include the output as text instead of an image? thanks Bruce On Mon, 7 Aug 2017, Sneha Pandya wrote: > > Hi Bruce, > > > Please find attached recon-all.log file and I used following command to run > the base: > > > recon-all -base ped1_base -tp ped1_0 -tp ped1_1 -tp ped1_2 -tp ped1_3 -tp > ped1_4 -all > > > Following is the screen shot of output showing the error: > > [IMAGE] > > Thanks, > Sneha > > ________________________________________________________________________________________________________________________________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl > <fis...@nmr.mgh.harvard.edu> > Sent: Monday, August 7, 2017 1:43:01 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Cortical thickness map for a pediatric case > Hi Sneha > > can you send us the commad you ran and the full screen output inluding > the error and also the recon-all.log? > > cheers > Bruce > > On Mon, 7 > Aug 2017, Sneha Pandya wrote: > > > > > Dear team, > > > > > > I have completed cross-sectional pipeline on my pediatric case with a > > baseline and 4 follow up time points between 4-7 years of age. However, I > > was not able > to > > run longitudinal pipeline on it as the base template creation failed with > > some topological errors. I assume this failure is due to large eTIV changes > > within > 4-7 > > years of age. > > > > > > I wanted to compare cortical thickness map of follow-up time points to its > > baseline using qdec. However, I was not able to as running qdec with single > > subject > > failed with 0 dof error. Can you'll please suggest how can I generate > > cortical thickness map between follow-up and baseline scans for this > > subject if qdec is > > not an option. > > > > > > Thanks, > > > > Sneha > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIBAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2 > s&r=AEsux002jQ5JzIPYIcsXKAuQmrt-1dubP8ZVldIiOrE&m=ZXdfsEFHvU5Da_0jY-5Y7dKAwDbjKKywa12mOg1QHAg&s=fvKw5PVmS-n5gHCflXKsLKtNc_cHzjNe6iBGWM2a1p4&e= > > > 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 > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DwIBAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=AEsux002jQ5JzIPYIc > sXKAuQmrt-1dubP8ZVldIiOrE&m=ZXdfsEFHvU5Da_0jY-5Y7dKAwDbjKKywa12mOg1QHAg&s=v5Rhqr82TUsnGS2hz-ynkgOBOKxOnkfOT8tIwEaW1xk&e= > . 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. > > >
base_ped1_base_screenlog
Description: base_ped1_base_screenlog
_______________________________________________ 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.
