Hi, thank you. I am using Linux. I not sure where to change path, ie which
file this should be done in and where this file is located. This the error
message I recieve, and as I said It is launching the wrong matlab and I
don't know how change this.
Launching Matlab7p13
Warning: Unable to open d
Dear Douglas,
Please, find attached aseg.stats files for subj1 and subj2.
Thanks
Daniel
aseg.stats_subj2
Description: Binary data
aseg.stats_suj1
Description: Binary data
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Dear Anastasia,
I tried the command you suggested me and i obtained the output I attach to the
mail.
I would like to ask you if I understood well shot it means. In this case left
uncinatus connects the following cortex areas:
ctx-lh-fusiform
ctx-lh-inferiortemporal
ctx-lh-lateralorbitofront
Dear Anastasia,I tried the command you suggested me and i obtained the output I attach to the mail.I would like to ask you if I understood well shot it means. In this case left uncinatus connects the following cortex areas:ctx-lh-fusiform ctx-lh-inferiortemporal ctx-lh-lateralorbitofrontalctx-lh-m
No, you mean anatomically speaking? If it's unfixable then that's OK, was just
wondering if it was possible.
> On Oct 22, 2013, at 10:14 PM, Bruce Fischl wrote:
>
> I'm not sure it's fixable then. Any idea what they are?
> Bruce
>
>
>
>> On Oct 22, 2013, at 9:30 AM, Jonathan Holt wrote:
>>
see http://dx.plos.org/10.1371/journal.pone.0038234
On 22 Oct 2013, at 18:18, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
Message: 2
Date: Tue, 22 Oct 2013 16:15:44 +
From: "West, John D."
Subject: [Freesurfer] Subject processing difference between computers
To: "freesurfer "
Message-I
Hi Rashmi
what version are you running? If 5.3, upload the subject and I'll take a
look
Bruce
On Tue, 22 Oct 2013, Rashmi Singh wrote:
Hello FreeSurfer experts,
I am trying to run recon all on my data set, but I got following error message.
Please help me understand the message and suggest so
yes, anatomically. And I would guess it's unfixable without tons of work
On
Wed, 23 Oct 2013, Jon Holt wrote:
No, you mean anatomically speaking? If it's unfixable then that's OK, was just
wondering if it was
possible.
On Oct 22, 2013, at 10:14 PM, Bruce Fischl wrote:
I'm not sure i
Hi Daniel, what is this in reference to? If this is a follow up on a
previous thread, please include the rest of the thread and the file in
the same email. I go through way too many emails to keep track of who's
doing what. thanks!
doug
On 10/23/13 4:13 AM, Daniel Ferreira wrote:
Dear Dou
Hi Linn,
If you are using tcsh, you have to edit the file $HOME/.cshrc (.shrc should
work as well) to add the following line:
setenv PATH $PATH:/YOUR_PATH_TO_MATLAB_BIN_DIRECTORY
Then close the terminal and open a new one. Use the env command to be sure that
your path has been modified, then
I have two sets of identical blocks within each fMRI run, so conditions
{1,2,3,4,5,1,2,3,4,5}, and there are three separate runs of the two blocks.
If I run the analysis treating each with the contrasts set up with this
numbering scheme (e.g. 3 vs 1 has two occurrences) , I get the following
outpu
Sorry. I meant to do that.
Original Message
From: Bruce Fischl
To: Arash Nazeri
Sent: Wed, Oct 23, 2013 8:25 am
Subject: Re: [Freesurfer] Projecting voxel intensities to a surface file
Hi Arash
can you cc the list on this type of email so that others can answer?
Particularly Mat
Hi Everyone,
I have some data where the skull striping hasnt worked properly and there are
some skull remaining. However, upon looking at the white and pial surfaces,
those look perfectly fine. My question is will the erroneous skullstriping
affect the supratentorial volume estimation ?
I will
Subha,
The erroneous skullstripping will not affect your volume estimates as
long as the surfaces look good.
Maritza
On Wed, 23 Oct 2013, Subhabrata
Chaudhury wrote:
Hi Everyone,
I have some data where the skull striping hasnt worked properly and there are
some skull remaining. However
Even the Supratentorial volume ? Supratentorial volume includes some structures
outside the surfaces ?
Thanks
Subha
- Original Message -
From: Bruce Fischl
Sent: 10/23/13 01:13 PM
To: Subhabrata Chaudhury
Subject: Re: [Freesurfer] skull striping error question
You should be fine if the
You should be fine if the surfaces aren't affected by the remaining skull
Bruce
On
Wed, 23 Oct 2013, Subhabrata Chaudhury wrote:
Hi Everyone,
I have some data where the skull striping hasnt worked properly and there are
some skull remaining.
However, upon looking at the white and pial surfa
Hi Lucia - The columns "NVoxels Volume_mm3" in the mri_segstats output are
the volumes of each of the structures in the aparc+aseg, so those columns
have nothing to do with the path. The last few columns, "Mean StdDev Min
Max Range", are related to the values in path.pd.nii.gz.
Hope this helps
Thanks Ed. This is consistent with the differences we are seeing as well. The
two super computers are very different platforms so it makes sense.
I think we'll have to reprocess all cases for ongoing studies on the newer
super computer in this case. Not the answer I was hoping for, but what I
Hi,
I have a question regarding cluster size thresholding using mri_glmfit-sim.
Namely, I have a sig.nii conjunction map that I made with mri_concat.
The analyses that serve as input to the conjunction map are done on a
custom surface template.
If I want to run mri_glmfit-sim, how would that work?
Hello FS experts,
I'm attempting to transform the Yeo2011 annotations (lh & rh) from
fsaverage to individual subjects so as to then sample the cortical maps to
subject surfaces using mri_label2vol. However, I'm getting the error in the
subject line when I put in the following commands:
*mri_surf2
The full error msg is not in the subject line. My guess is that the
"lh." in front of "Yeo" in the srcsurfval is causing the problem
On 10/23/2013 03:17 PM, Paul Beach wrote:
> Hello FS experts,
>
> I'm attempting to transform the Yeo2011 annotations (lh & rh) from
> fsaverage to individual su
Hi,
I'm experiencing a problem when running the automated hippocampal subfield
segmentation script. Unfortunately, I have been unable to determine the
cause of the error. After reconstructing all participant data with the
-hippo-subfields flag, I ran the
"kvlQuantifyHippocampalSubfieldSegmentation
Apologies: the full error message was:
'*could not determine type of lh.Yeo2011_17Networks_N1000.annot*'
I tried your suggestion of removing the hemispheric designation in front of
'Yeo' and I'm getting the same error - - the same occurs if I remove the
'.annot' at the end.
*mri_surf2surf --srcsu
try specifying --sval-annot Yeo2011_17Networks_N1000.annot instead of
--srcsurfval
cheers
Bruce
On Wed, 23 Oct 2013, Paul Beach wrote:
Apologies: the full error message was: 'could not determine type of
lh.Yeo2011_17Networks_N1000.annot'
I tried your suggestion of removing the hemispheric des
That worked like a charm.
Thanks!
On Wed, Oct 23, 2013 at 5:14 PM, Bruce Fischl wrote:
> try specifying --sval-annot Yeo2011_17Networks_N1000.annot instead of
> --srcsurfval
>
> cheers
> Bruce
>
> On Wed, 23 Oct 2013, Paul Beach wrote:
>
> Apologies: the full error message was: 'could not det
Hi, When trying freeview command (see below) from the “Testing your
freesurfer installation” page using my own data, freesurfer opened, but I
am concerned about the “invalid drawable” lines. The message happened when
I ran this command on the "bert" data too. What does invalid drawable mean?
[Co
You can just ignore this warning message on Mac.
Best,
Ruopeng
On Oct 23, 2013, at 8:52 PM, Elissa McIntosh wrote:
> Hi, When trying freeview command (see below) from the “Testing your
> freesurfer installation” page using my own data, freesurfer opened, but I am
> concerned about the “inval
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