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
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
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:
[cid:8a9a6e17-acc5-4ddf-bb4e-c7c1ad8d8b3d]
Thanks, Sneha ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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_complia... . 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.
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.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... 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_complia... 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.
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... 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_complia... 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.
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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.edu
freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
mailman_listinfo_freesurfer&d=DwIBAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2 qu2
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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_complia...
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.
Thank you Bruce, sure thing :)
Regards,
Sneha
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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.edu
freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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_complia...
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.
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.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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.edu
freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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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.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.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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... 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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.edu
freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwMFaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=AEsux002jQ5JzIPYIcsXKAuQmrt-1dubP8ZVldIiOrE&m=dCfrEXilLmvgz6nyI1BNvXEFPlqVR6KxGcGjy1iQm6Y&s=i5HyyOqvoz-25jSUaDKeocMoc4griFQs_F00J1PKhNY&e=
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sneha Pandya snp2003@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-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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