Hi Martin,
Sorry for delayed response and thank you so much for looking into it. I will follow the steps as described to get their thickness maps.
For qdec, can we do analysis for single subjects? I believe I had tried it earlier but it failed with dof = 0. Can I set up qdec table as below to compute thickness map between thickness differences across time and base time point?
fsid age diagnosis subj_tp1minustp0 4 PatientTP subj_tp0 3 PatientBL
Thanks again,
Sneha
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Martin Reuter mreuter@nmr.mgh.harvard.edu Sent: Thursday, August 10, 2017 4:40:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical thickness map for a pediatric case
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 <snp2003@med.cornell.edumailto:snp2003@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@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.e...
Thanks,
Sneha
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@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
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