, Crawford, Anna wrote:
External Email - Use Caution
Hello,
I am trying to run the PetSurfer process for the first time. I was able to run
gtmseg and mri_coreg which seemed to go okay. When I tried running mri_gtmpvc,
it is crashing, but I am not sure why. The command I am using and output
External Email - Use Caution
Hello,
I am trying to run the PetSurfer process for the first time. I was able to run
gtmseg and mri_coreg which seemed to go okay. When I tried running mri_gtmpvc,
it is crashing, but I am not sure why. The command I am using and output are
below.
Hi Anna,
See attached.
Lilla
On Fri, 25 Oct 2019, Crawford, Anna wrote:
>
> External Email - Use Caution
>
> Hello,
>
>
> Just a quick question. We recently installed the new thalamus segmentation
> subroutine. It's really wonderful, and much promise to
External Email - Use Caution
Hello,
Just a quick question. We recently installed the new thalamus segmentation
subroutine. It's really wonderful, and much promise to our work.
I can't find a lookup table with the numerical labels from the FS output to the
thalamic nuclei. Th
hu, 11 Apr 2019, Crawford, Anna wrote:
>
> Hello,
>
>
> I was looking to use the Freesurfer infant brains pipeline. I have found it
> used with 3T data, but I was wondering if it can be used with 1.5T data as
> well.
>
>
> Thanks,
>
> Anna
>
>
> Please c
External Email - Use Caution
Hello,
I was looking to use the Freesurfer infant brains pipeline. I have found it
used with 3T data, but I was wondering if it can be used with 1.5T data as well.
Thanks,
Anna
Please consider the environment before printing this e-mail
Clevela
: freesurfer@nmr.mgh.harvard.edu
Subject: [EXT] Re: [Freesurfer] Re: Re: Re: Re: Time Series to Surface
Can you upload the volume (img and hdr) here:
https://gate.nmr.mgh.harvard.edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2>
On 4/6/18 12:24 PM, Crawford, Anna wrote:
1227
frames are in your input file? Eg, if you run mri_info on it?
On 4/6/18 12:05 PM, Crawford, Anna wrote:
> I just opened freeview and loaded everything in the GUI. I did not use the
> command line to open it. I do not see a slider bar.
>
> Th
: freesurfer@nmr.mgh.harvard.edu
Subject: [EXT] Re: [Freesurfer] Re: Re: Time Series to Surface
what is your freeview command line? Do you see a "frame" slider bar?
On 4/6/18 10:46 AM, Crawford, Anna wrote:
> I tried without --init-fsl and adding in the --projfrac 0.5 for mri_vol2s
AM, Crawford, Anna wrote:
> Hello,
>
> I used the following commands and then opened the surface as an overlay on
> the inflated volume, but I am not about to look at the time series. The view
> time course is grayed out so that I can not click on it. Did I miss a step or
> lo
freeview
On 04/05/2018 01:49 PM, Crawford, Anna wrote:
> Hello,
>
> I have a time series (.hdr/.img) that I want to overlay onto a
> surface, specifically the inflated surface from the anatomy. I suspect
> I have to use mri_vol2surf, which requires a source registration
> file. How
Hello,
I have a time series (.hdr/.img) that I want to overlay onto a surface,
specifically the inflated surface from the anatomy. I suspect I have to use
mri_vol2surf, which requires a source registration file. How do I get this
file? Then once I have this file, will I be able to view step by
Hello,
i am using the hippocampal subfield segmentation. I am looking at the results
in [lr]h.hippoSfVolumes-T1.v10.txt. I saw the following in the FAQs and was
unsure of what the units were then in the .txt file. Does the .txt file give
units in mm^3?
* The sum of the number of voxels
, usually the white, eg,
mris_inflate -n 5 -no-save-sulc lh.white lh.inflated.anna
On 03/01/2017 11:45 AM, Crawford, Anna wrote:
> I did:
>
> mris_inflate -n 5 wmparc.mgz inflateTest.mgz
>
> I wasn't sure oh what my input file should be. It resulted in the following
> me
lf of Douglas N Greve
Sent: Wednesday, March 1, 2017 11:41 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Inflated Volume
what is your mris_inflate command line?
On 03/01/2017 11:20 AM, Crawford, Anna wrote:
>
> Hi,
>
>
> I am using a volume to create a surface ove
Hi,
I am using a volume to create a surface overlay. I am currently overlaying onto
the ?h.inflated volumes created when recon-all is executed. These volumes are
overinflated for what I want. Is there a way I can create a less inflated,
inflated-volume? I was looking at mris_inflate, and was t
:53 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Remapping Volume
Try adding --projfrac 0.5
On 10/12/2016 11:29 AM, Crawford, Anna wrote:
> I did:
>
> mri_vol2surf --src
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/mri/aparc+asegRMnn.mgz
>
of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, October 11, 2016 10:29 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Remapping Volume
what was your vol2surf command line? Make sure that it is using nearest
neighbor interpolation
On Tue, 11 Oct 2016, Crawford, Anna wrote:
&g
some bbregister-generated .dat file with PET
data.
cheers
Bruce
On Fri, 30 Sep 2016, Crawford, Anna wrote:
> No problem. I'm not exactly sure, but I think I just want a surface overlay
> so mri_vol2surf would be what I want. Right now, I am just trying to get
> down the generic way of
o
the values in $FREESURFER_HOME/FreeSurferColorLUT.txt, eg, left superior
temporal gyrus should be
1030ctx-lh-superiortemporal 140 220 220 0
On 09/30/2016 04:15 PM, Crawford, Anna wrote:
> I did the same thing usng aparc+aseg.mgz and added --projfrac 0.5 and I got a
> simi
color scale will be different)
On 09/30/2016 03:51 PM, Crawford, Anna wrote:
> I was just using the wmparc as an example to get a volume overlay onto the
> surface. I chose that one just to see the parcellated surface similar to the
> volume.
> ___
ation boundaries
right at the surface, so the actual value there will be unpredicatable.
On 09/30/2016 03:31 PM, Crawford, Anna wrote:
> Thank you everyone for your help! I do have a follow up question. I believe
> this did what I wanted and is what I will want to do for PET data for
> e
ndidate
McGill University
Integrated Program in Neuroscience
Psychology
On Fri, Sep 30, 2016 at 12:46 PM, Crawford, Anna
mailto:crawf...@ccf.org>> wrote:
Yeah, I get Error: Option unknown for --regmethod
Anna
From:
freesurfer-boun...@nmr.mgh.har
: Freesurfer support list
Subject: Re: [Freesurfer] Volume to Surface
hmmm, yup not sure there. Did you try "--regmethod subject"
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Fri, Sep 30, 2016 at 12:14 PM, Crawford, Anna
mailto:crawf...@ccf.org>
n Fri, Sep 30, 2016 at 11:22 AM, Crawford, Anna
mailto:crawf...@ccf.org>> wrote:
I am still having problems. If I do --reg subject I get an error back that it
is a directory. If I pick a specific file such as orig.mgz (default according
to help file), I get the same error as befor
mri_vol2surf with
--regmethod subjid since you don't actually want to perform a transformation.
Maybe try that?
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Fri, Sep 30, 2016 at 10:54 AM, Crawford, Anna
mailto:crawf...@ccf.org>> wrote:
No p
s that already exist.
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Fri, Sep 30, 2016 at 10:44 AM, Crawford, Anna
mailto:crawf...@ccf.org>> wrote:
I already ran recall-all. I am trying to create a different surface not creat
, Crawford, Anna
mailto:crawf...@ccf.org>> wrote:
Hello,
I am trying to take nay volume that is registered and create an inflated
surface. I am trying to use mri_vol2surf. I am having problems with the
registration source. From the examples I could fine, it should be --srcreg
*.dat. Th
Hello,
I am trying to take nay volume that is registered and create an inflated
surface. I am trying to use mri_vol2surf. I am having problems with the
registration source. From the examples I could fine, it should be --srcreg
*.dat. The only *.dat file I have is segment.dat which does not work
: Thursday, September 29, 2016 1:14 PM
To: Douglas N Greve
Cc: freesurfer@nmr.mgh.harvard.edu; Crawford, Anna; Anna Crawford
Subject: Re: [Freesurfer] Infalted/Label
you can also look at the vertex index of the first entry in the label
file and type that into the "cursor" field in freev
or the volume I would
imagine.
Thanks,
Anna
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, September 29, 2016 1:13 PM
To: Crawford, Anna; Bruce
on of the label
isn't on the surface though.
Thank you!
Anna
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, September 29, 2016 12:45 PM
To: Crawford, Anna; Bruce Fischl
Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu
Subject: Re
Testing1N.label 216
mri_label2label: Done
Thanks,
Anna
From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Thursday, September 29, 2016 12:29 PM
To: Crawford, Anna
Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve
Subject: RE: Infalted/Label
I'
, use --regmethod surface
On 09/28/2016 04:39 PM, Crawford, Anna wrote:
> The subject path was
> /mnt/netScratch/crawforda/Brainstem/study11074/S2sdt/segfs/surf
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.ha
28, 2016 4:35 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Co-registering different source data
which lh.inflated and rh.inflated did you load? That is, for which
subject?
On Wed, 28 Sep 2016, Crawford, Anna wrote:
> I just opened freeview (just typed freeview into the command l
: [Freesurfer] Co-registering different source data
what was your freeview command line, and what did you do to make it crash?
On Wed, 28 Sep 2016, Crawford, Anna wrote:
> Thank you! that seemed to have worked. I thought I had tried that before, but
> must not that. The input/output is belo
, 2016 4:08 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Co-registering different source data
Try giving it the full path to the label, ie,
--srclabel
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
On 9/28/16 3:47 PM, Crawford, Anna wrote:
>
d you tried to run and the error it gives?
thanks
Bruce
On
Tue, 27 Sep 2016, Crawford, Anna wrote:
> I have tried multiple variations for my subject directory. I have had it end
> at study11074, S2sdt, segfs, and label. I suspected it should either be S2sdt
> or segfs. I get the same erro
el
I suspect the value should be:
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
or possibly something else:
${SUBJECTS_DIR}/$SUBJECT/label/
should be the directory with Testing.label
hth
d
On 9/27/16 11:58 AM, Crawford, Anna wrote:
> Th output is below:
>
> aparc.ann
: [Freesurfer] Co-registering different source data
what is the output of "ls"?
On 9/27/16 11:50 AM, Crawford, Anna wrote:
> Thank you. That worked for changing the default directory. When I run
> mri_label2label, I am still getting the same error that there is no such file
> o
...@nmr.mgh.harvard.edu] on behalf of dgw [dgwake...@gmail.com]
Sent: Tuesday, September 27, 2016 11:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Co-registering different source data
Anna, if you are using bash the command is:
export SUBJECTS_DIR=
On 9/27/16 11:31 AM, Crawford, Anna wrote
I also tried doing setenv SUBJECTS_DIR but that did not work either.
bash: setenv: command not found
Thanks,
Anna
From: Crawford, Anna
Sent: Tuesday, September 27, 2016 11:12 AM
To: Freesurfer support list
Subject: RE: [Freesurfer] Co-registering
t use the --sd.
On 9/27/16 9:38 AM, Crawford, Anna wrote:
> Hi,
>
> I keep getting an error when I use mri_label2label. Below is my input and
> output. I have tried various paths all the way down to the label and above
> the subject level, but still always get the same error. I have
o the
inflated surface in freeview
cheers
Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
> Hi,
>
> i created a test ROI which saves as a label. Every time I try to load it as a
> label on the surface (inflated), it crashed FreeView. I'm not sure why it
> won't load
ource data
Hi Anna
scuba is very old and deprecated. Try using freeview instead
cheers
Bruce
On Mon, 26 Sep
2016, Crawford, Anna wrote:
> To create the volume ROI, I found something that said to use:
>
> scuba -v $filename
>
> to then make a new ROI.
>
> I got en error that
data
yes, create a volume ROI and you can map it onto the surface using
mri_vol2surf
cheers
Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
> For now, I am just trying to get any arbitrary ROI that I define. (I'm new to
> this and am just trying to figure out how to get th
ering different source data
can you explain what the ROI is supposed to represent? If you can create
it in the volume, you can use mri_vol2surf to map it onto the surface.
cheers
Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:
> Hi,
>
> I am having trouble figuring out how to create my
then you can visualize them on the inflated
surface trivially. That is, you can create your ROI on any surface of the
same hemisphere/subject and visualize it on any other
cheers
Bruce
On Mon, 26 Sep 2016, Crawford, Anna
wrote:
> Hello,
>
> I am trying to create a new surface area o
Hello,
I am trying to create a new surface area on the inflated brain given by
freesurfer using recon-all. I make to create my own ROI that is co-registered
onto this surfer. Ultimately, I want to be able to take information from a
different data source such as EEG and have it co-registered ont
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