Resolved - thank you Andrew!
Solution: operator error, needed to cat file w/ input list for --inputs instead
of just specifying file w/ input list
From: Hoopes, Andrew
Sent: Thursday, February 15, 2018 4:43:18 PM
To: Makaretz, Sara Johanna; Freesurfer support
Hi Andrew,
python --version
=
Python 2.7.3 -- EPD 7.3-1 (64-bit)
Sara
From: Hoopes, Andrew
Sent: Thursday, February 15, 2018 3:56:22 PM
To: Makaretz, Sara Johanna; Freesurfer support list
Subject: Re: [Freesurfer] IndexError: list index out of range
Hi Sara
___
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Makaretz, Sara Johanna
Sent: Tuesday, February 13, 2018 10:12:07 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] IndexError: list index out of range
Hi Doug,
I am also getting the error "IndexError
Hi Doug,
I am also getting the error "IndexError: list index out of range" - I got the
same error using FS6.0/FS5.3/dev. This is what I'm running for asegstats2table:
asegstats2table --common-segs -t aparc.a2009s+aseg.max.table -i
aparc.a2009s+aseg.lst -m max
Parsing the .stats files
Traceba
Hi FS group,
My goal is to calculate the % of voxels in a given region that are higher than
a region-specific threshold. This is what I've done so far for each subject:
* recon T1
* coregister vol.nii to T1
* move aparc+aseg.mgz into functional space
* mri_segstats --i vol.nii
Hi Doug,
I'm still stuck on this subject and am wondering if you have any advice.
Thanks for any help!
Sara
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Makaretz, Sara Johanna
Sent: Friday, December 15, 2017 12:04:48 PM
To: frees
Hi Doug,
I ran mri_gtmseg on a subject & got no errors, and the gtmseg.mgz/apas+head.mgz
outputs looked fine:
$Id: mri_gtmseg.c,v 1.9.2.1 2016/08/02 21:07:49 greve Exp $
mri_gtmseg --s $s
etc, exited fine
Then I tried running mri_gtmpvc, and got a 'failed tissue type check' error:
[weckl:FDG_201
Hi Lorenzo,
I was trying to do this too, and used:
1. mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi $h
--sval-annot $h.yeo.annot
--tval $SUBJECTS_DIR/$s/label/$h.yeo.annot
2. make yeo.gtmseg.ctab - I copied gtmseg.ctab, pasted yeo net
Still wondering about this - thanks in advance for any help!
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Makaretz, Sara Johanna
[smakar...@mgh.harvard.edu]
Sent: Thursday, June 01, 2017 21:30
To: Freesurfer
Hi,
I'm using FS v6.0 stable. Is there any difference between running recon-all
with -autorecon2-wm or -autorecon-noaseg? It looks like both are starting at
-normalization2 and running through the rest of autorecon2 with no changes to
inputs/args compared to "regular" -autorecon2.
Is this true
o fsaverage. This is probably not the intent of
people who are specifying a target, so I changed mris_preproc to require
a targets-specific registration. You can generate this with
surfreg --s subject --t target
then run mris_preproc specifying the given target
doug
On 05/24/2016 04:23 PM, Makaretz
Hi Doug, still wondering about this - thanks!
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Makaretz, Sara Johanna
[smakar...@mgh.harvard.edu]
Sent: Tuesday, May 24, 2016 16:23
To: Freesurfer support
gs baby so
>I suggest just posting this question to the list with "mris_preproc" in
>the subject, and I bet he will give you the answer.
>
>-Zeke
>
>On 05/23/2016 10:31 PM, Makaretz, Sara Johanna wrote:
>> Hi Zeke,
>>
>> I am running some surface glms
, Makaretz, Sara Johanna wrote:
> Hi, I want to map a label from one hemi to the other (all on
> fsaverage). I tried mri_label2label:
>
> mri_label2label --s fsaverage --srchemi lh --trghemi rh --srclabel
> lh.a.label --trglabel rh.flipped_lh.a.label --regmethod surface
>
>
I'm actually wondering the same thing re AAL to subject space - this is what I
have been using:
spmregister - reg template to subject
mri_label2vol - move AAL to subject space
mri_segstats - pull in-volume stats using AAL in subject space
mri_vol2surf - project AAL (subject space) to subject surf
Hi, I want to map a label from one hemi to the other (all on fsaverage). I
tried mri_label2label:
mri_label2label --s fsaverage --srchemi lh --trghemi rh --srclabel lh.a.label
--trglabel rh.flipped_lh.a.label --regmethod surface
but I think I need to specify a reg file to go between hemispheres
Hi all, I am having a problem with moving aparc+aseg to different dimensions. I
have successfully resliced aparc+asegs for several other subjects, but the
resliced volume for one subject appears cut-off at the bottom. The dimensions
match for this subject's template and output volumes, and the o
Hi,
I have a PET volume that is registered to a recon, then projected to the
surface via vol2surf. I would like to pull stats for the PET using aparc
regions. Should I use mri_annotation2label, then pull stats for each label? Or
is there something similar to mri_segstats, ie. --annot lh.aparc.an
Hi all,
I ran mri_cvs_register but forgot to add --nocleanup. I have the final
combined m3z and no tm3d, and for el_reg just mgz files. Can I recreate
the tm3d combined with just these files?
On the wiki it says use createMorph - I tried different inputs in 5.3
and dev environments with no succes
problem with the skull stripping. If you
> clone the brain voxels back in and rerun do things work?
>
>> On Aug 11, 2014, at 4:11 PM, "Makaretz, Sara Johanna"
>> wrote:
>>
>> I am having trouble getting a usable brainmask for one of my subjects -
>&g
Hi all,
I like the excel presentation of the recon-all process/files table for
Freesurfer 3.0.5 found here:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllFilesVsSteps
Is there an updated document for a more recent version? (I am using 5.3.0)
Also, are 5.2 and 5.3 similar enough to reference
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