Hi Sneha, I don’t know why this fails. There could be many reasons. Firstmost, the longitudinal stream assumes that head size is constant, which is probably not the case in your data. Looking at the log file however, it seems that recon-all stops in the NU correction step that comes before talairach registration and it is unclear why.
Take a look at the orig.mgz (the template image). If that looks bad, like to shadow images that don’t align, then the robust_template registration code fails before. If it looks like a brain (maybe a little blurry, but otherwise OK), then It would be the NU correct. Anyway I don’t think you should spend to much time debugging for the reason above. Instead you could simply use the cross sectional stream. Then register all thickness files to fsaverage (mri_preproc), then do a pairwise subtract or Percent change computation and after that a group analysis on the thickness differences across time. I think mri_concat can do pairwise differences. And you would have to setup the GLM on your own with mri_glmfit or create a qdec table where you only have one entry per subject. Best, Martin > On 10. Aug 2017, at 17:02, Sneha Pandya <snp2...@med.cornell.edu> wrote: > > 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= > > > > <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_ > > > > > ><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 > > > > > ><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. > > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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