On 6/5/2020 4:47 PM, Sneha Pandya wrote:
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Thank you Doug.
it is not run by default
* When I ran “samseg2recon –s subject” after running samseg, it did
not do anything different, am I missing anything?
What do you mean it did not do anything different? What is your samseg
command?
*
Yes, a lot of file names changed. You should look at the seg.stats file
* We did not get seg.stats as an output file when we ran 2019 dev
version. We just got samseg.stats under subject/mri/samseg folder.
In that case which file should we consider, or something went
wrong if it did not generate this file.
the samseg.stats file has been renamed to seg.stats
Besides, when we ran samseg in 2019 we had used mri/T1.mgz file as an
input. Will this be a problem based on your suggestion in *MailScanner
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* Should we rerun our subjects with orig.mgz or with raw dicom or
nifti file?
Use the orig.mgz, not the T1.mgz. file format is unimportant
*
Thank you,
Sneha
*From: *Douglas N. Greve <mailto:dgr...@mgh.harvard.edu>
*Sent: *Friday, June 5, 2020 4:05 PM
*To: *freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *[EXTERNAL] Re: [Freesurfer] samseg with subfields {Disarmed}
On 6/5/2020 3:54 PM, Sneha Pandya wrote:
* External Email - Use Caution *
Dear Dough,
Is samseg2recon run by default when we run just samseg command?
After samseg is completed it displays towards the end samseg2recon
run time in sec and hours, right before computation time of samseg
as below. If it is called by samseg command itself there would be
no need to run samseg2recon separately after samseg command right
unless it is doing something in addition?
Started at Fri Jun 5 12:49:50 EDT 2020
Ended at Fri Jun 5 12:51:57 EDT 2020
Samseg2recon-Run-Time-Sec 127
Samseg2recon-Run-Time-Hours 0.04
samseg2recon Done
Started at Fri Jun 5 12:27:43 EDT 2020
Ended at Fri Jun 5 12:51:57 EDT 2020
Samseg-Run-Time-Min 24.23
Samseg-Run-Time-Hours 0.40
it is not run by default.
I had ran few subjects with samseg from Freesurfer dev version in
Oct of 2019 and compared it with samseg version from Freesurfer
v7.1.0 and realized that some file names are different. Samseg
from dev version I ran in 2019 created file t1w_biasCorrected.nii,
t1w_biasField.nii, t1w_crispSegmentation.nii names under
saubject/mri/samseg directory and Freesurfer v7.1.0 creates
mode01_bias_corrected.mgz, mode01_bias_field.mgz, seg.mgz files. I
assume these files should be comparable across these two versions
right? Also, I do not see seg.stats file when I ran with dev
version in 2019. Which stat file am I suppose to consider in lieu
of seg.stats file when I ran with 2019 dev version?
Yes, a lot of file names changed. You should look at the seg.stats file
Besides, when we ran samseg in 2019 we had used mri/T1.mgz file
as an input. Will this be a problem based on your suggestion in
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Thank you,
Sneha
*From: *Douglas N. Greve <mailto:dgr...@mgh.harvard.edu>
*Sent: *Tuesday, May 5, 2020 11:38 AM
*To: *freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *[EXTERNAL] Re: [Freesurfer] samseg with subfields
In theory it is possible, though I don't know if it is better or
worse. You can run samseg, then run samseg2recon (this creates a
folder that looks like it was created by recon-all), then run
subfields on that folder
On 5/5/2020 10:45 AM, Sneha Pandya wrote:
* External Email - Use Caution *
Dear experts,
I want to revisit if anyone has ran subfield analysis just by
running samseg? If it is possible is it as reliable as from
running regular routine with “-all” recon-all flag?
Thank you,
Sneha
*From:* Sneha Pandya
*Sent:* Thursday, April 30, 2020 4:15 PM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* samseg with subfields
Dear experts,
Is it possible to run subfield analysis (hippcampal subfields,
amygdalar, thalamic nuclei, and brainstem structures) when we
only run samseg on our dataset?
Thank you,
Sneha
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