Re: [Freesurfer] Cortical thickness map for a pediatric case {Disarmed}
Hi Martin,
I followed step as you suggested to get pairwise difference steps but I believe
I am missing something for qdec.
1. I did not run mris_preproc to register all thickness files to fsaverage as I
had already ran by cross-sectional pipeline with -qcache flag. I also see all
rh.volume.fwhm[5,10,15,20,25].fsaverage.mgh
lh.volume.fwhm[5,10,15,20,25].fsaverage.mgh thickness maps under surf folder
for each subject. So not doing mris_preproc should be fine right?
2. I used mri_concat to compute pairwise differences in thickness maps for each
hemisphere between base tp and follow up tp by doing following:
mri_concat --i base_subj/surf/rh.thickness.fwhm10.fsaverage.mgh \
--i first_tp_subj/surf/rh.thickness.fwhm10.fsaverage.mgh \
--o out_subj/surf/rh.base-first_tp.thickness.fwhm10.fsaverage.mgh \
--paired-diff
3. Please note I created a septate folder (out_subj) and saved pairwise
difference maps inside out_subj/surf folder. I Then created a qdec folder
inside out_subj folder and prepared qdec.dat.file(used demeaned age)
fsid age
qdec_ped1_1 -0.5
4. In design tab, I then used age as a covariate and ran analyze with fwhm as
10 and thickness for measure. At this point it shows an error:
Couldn't open out_subj/surf/lh.thickness.fwhm10.fsaverage.mgz or .mgh file.
Can you please suggest what am I missing or doing wrong? Am I suppose to create
.Qdecrc inside qdec folder as suggested in earlier archives, or is it because I
am saving pairwise difference maps in a completely different folder?
Thanks,
Sneha
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Sneha Pandya
<snp2...@med.cornell.edu>
Sent: Thursday, August 17, 2017 11:57:40 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical thickness map for a pediatric case {Disarmed}
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Martin Reuter
<mreu...@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
<snp2...@med.cornell.edu<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Bruce Fischl
<fis...@nmr.mgh.harvard.edu<mailto: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
Re: [Freesurfer] Cortical thickness map for a pediatric case {Disarmed}
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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Martin Reuter <mreu...@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 <snp2...@med.cornell.edu<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu<mailto: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_b
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 <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
Re: [Freesurfer] Cortical thickness map for a pediatric case
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=DwIDbA=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=AEsux002jQ5JzIPYIcsXKAuQmrt-1dubP8ZVldIiOrE=BoRZLsXqqVT6-Qe8baTB-uaC5VkO8MylpF2Pge0ejiI=80fR0T3L4F8R5icMg6uqKyEXyWyEbcpI5AFOF2UVRzo= > > > 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 > > > >______________ > _
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=DwIDbA=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=AEsux002jQ5JzIPYIcsXKAuQmrt-1dubP8ZVldIiOrE=BoRZLsXqqVT6-Qe8baTB-uaC5VkO8MylpF2Pge0ejiI=80fR0T3L4F8R5icMg6uqKyEXyWyEbcpI5AFOF2UVRzo= > > > 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
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 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 > > > > > > > > > __
Re: [Freesurfer] Cortical thickness map for a pediatric case
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.harv
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=DwIBAg=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2 s=AEsux002jQ5JzIPYIcsXKAuQmrt-1dubP8ZVldIiOrE=ZXdfsEFHvU5Da_0jY-5Y7dKAwDbjKKywa12mOg1QHAg=fvKw5PVmS-n5gHCflXKsLKtNc_cHzjNe6iBGWM2a1p4= 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=DwIBAg=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=AEsux002jQ5JzIPYIc sXKAuQmrt-1dubP8ZVldIiOrE=ZXdfsEFHvU5Da_0jY-5Y7dKAwDbjKKywa12mOg1QHAg=v5Rhqr82TUsnGS2hz-ynkgOBOKxOnkfOT8tIwEaW1xk= . 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 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.
[Freesurfer] Cortical thickness map for a pediatric case
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://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.
