...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Wednesday, October 27, 2021 10:07 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Local GI MRI_segstats error
Try removing the trailing slash (/) from the subject name after --annot
On 10/19/2021 9:24 AM, COLLEEN PLETCHER wrote
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Hello,
I am trying to run mri_segstats for local GI indices. I am getting a file not
found error for /tmp/mri_segstats.tmp.sub-1007_ses_01/.lh.176.ctab
I did not get an error message when running the recon-all -localGI command and
I am using freesur
of COLLEEN PLETCHER
Sent: Tuesday, May 11, 2021 4:28 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error
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Hello,
Getting a list of the labels would be fantastic! Also, when relabeling the
segmentations, do you
send you a list of lables
that get generated by our tool and then you can match those up with the ones
that you get with FSL.
Best, Lilla
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of COLLEEN PLETCHER
Sent: Tuesday, April 27, 2021 4:11 PM
To
aseg lables in your input segmentation file?
Lilla
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of COLLEEN PLETCHER
Sent: Friday, April 23, 2021 3:01 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error
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Hi,
Just checking in about this question. Please let me know if you need anything
else from me!
Thanks,
Colleen
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of COLLEEN PLETCHER
Sent: Tuesday, April 13
: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of COLLEEN PLETCHER
Sent: Tuesday, April 13, 2021 1:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Infant Freesurfer exiting without error
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Hi,
I am trying to run infant freesurfer using the
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Hi,
I am trying to run infant freesurfer using the --segfile and --masked options.
When I attempt to run it, it runs for a bit and then I get this:
USAGE: mri_or fname1 fname2 ..
After this, the program exits. I am not getting any error, so I a
dable: (chmod 777 -R)
check in the base-tps that all time points are listed correctly
check that names have no underscores '_'
try re-running -base
also:
check the names of subjects in the command (recon-all -long ...)
A.
Le mar. 9 juin 2020, à 11 h 04, COLLEEN PLETCHER
Alex
Le mar. 9 juin 2020, à 10 h 26, COLLEEN PLETCHER
mailto:ccpletc...@medicine.wisc.edu>> a écrit :
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Hello,
I am currently attempting to run a brain through the longitudinal stream after
performing edits on the longitudinal brain, using the command
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Hello,
I am currently attempting to run a brain through the longitudinal stream after
performing edits on the longitudinal brain, using the command recon-all -long
timepoint1 base -autorecon2-wm -autorecon3. I am getting an error that says
Unmatched
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That would be great, thank you!
Colleen Pletcher
coll...@tpck.net
> On Apr 24, 2020, at 3:58 PM, Lilla Zollei wrote:
>
>
> No, but I can definitely keep you in the loop.
> Lilla
>
>> On Wed, 22 Apr 2020, COLLEEN PLET
: Freesurfer support list
Subject: Re: [Freesurfer] Infant freesurfer
Yes, I would like to add it.
Lilla
On Wed, 22 Apr 2020, COLLEEN PLETCHER wrote:
>
> Ok, thank you! Do you think this option will eventually be
: Re: [Freesurfer] Infant freesurfer
Hi Colleen,
The manual editing option has not yet been added to the pipeline.
Best, Lilla
On Wed, 22 Apr 2020, COLLEEN PLETCHER wrote:
>
> Hello. I am working with the infant Freesurfer pipeline. I have noticed that
> some of our subjects may n
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Hello. I am working with the infant Freesurfer pipeline. I have noticed that
some of our subjects may need to be manually edited, and then run through the
pipeline again. However, when I try to do an infant_recon_all command combined
with something l
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