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
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Makaretz, Sara Johanna
<smakar...@mgh.harvard.edu>
Sent: Tuesday, February 13, 2018 10:12:07 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] IndexError: l
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
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
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Makaretz, Sara Johanna
<smakar...@mgh.ha
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:
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
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
be done to 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
ont know the answer. mris_preproc is Dougs 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,
>>
>&g
, 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
>
&g
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
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
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
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
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
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
smakar...@mgh.harvard.edu wrote:
I am having trouble getting a usable brainmask for one of my subjects -
a screenshot of the initial brainmask.mgz is attached
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
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