Hi Bruce and Martin,
Wanted to follow up and see if you'll got a chance to look at the error and if I could try out something? Thanks, Sneha ________________________________ From: Sneha Pandya Sent: Tuesday, August 8, 2017 11:29:23 AM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical thickness map for a pediatric case Thank you Bruce, sure thing :) Regards, 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 6:21:57 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical thickness map for a pediatric case thanks Sneha you'll probably need to wait until tomorrow for Martin to read his email :) cheers Bruce On Mon, 7 Aug 2017, Sneha Pandya wrote: > > 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 > https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu_fswiki_BugReporting&d=DwIDbA&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=AEsux002jQ5JzIPYIcsXKAuQmrt-1dubP8ZVldIiOrE&m=BoRZLsXqqVT6-Qe8baTB-uaC5VkO8MylpF2Pge0ejiI&s=80fR0T3L4F8R5icMg6uqKyEXyWyEbcpI5AFOF2UVRzo&e= > > > 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-RXrryqt9KZX2 > qu2 > >s&r=AEsux002jQ5JzIPYIcsXKAuQmrt-1dubP8ZVldIiOrE&m=ZXdfsEFHvU5Da_0jY-5Y7dKAwDbj > KKywa12mOg1QHAg&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_complianc > eline&d=DwIBAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=AEsux002jQ5JzIP > YIc > >sXKAuQmrt-1dubP8ZVldIiOrE&m=ZXdfsEFHvU5Da_0jY-5Y7dKAwDbjKKywa12mOg1QHAg&s=v5Rh > qr82TUsnGS2hz-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. > > > > > > > >
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