I checked version of recon-all script using 'recon-all -version’ command
and 'freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c’ is printed.
Juhyoung
> On Feb 9, 2017, at 1:02 PM, Bruce Fischl wrote:
>
> What does
>
> which recon-all
>
> return?
>
>> On Feb 8,
What does
which recon-all
return?
> On Feb 8, 2017, at 10:54 PM, Juhyoung Ryu wrote:
>
> Yes, I set FREESURFER_HOME variable as '/Applications/freesurfer’, which I
> installed freesurfer v6.
> I attached recon-all.log file below.
> I can see 'build-stamp.txt:
Yes, I set FREESURFER_HOME variable as '/Applications/freesurfer’, which I
installed freesurfer v6.
I attached recon-all.log file below.
I can see 'build-stamp.txt: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c’ in
log file.
Is there anything to check more?
Thank you,
Juhyoung
Hi Qian
if you look at the recon-all help you will see:
USAGE: recon-all
Required Arguments:
-subjid
-
Fully-Automated Directive:
-all : performs all stages of cortical reconstruction
-autorecon-all : same as -all
Manual-Intervention Workflow Directives:
-autorecon1
Hi Bruce,
I am a little confused about it. I found 'Manual-Intervention Workflow
Directives' on recon-all free surfer wiki web.
It said if edits made to correct pial, run-autorecon2-pial.
If I only edit pial, I run >recon-all -autrecon-pial -s -sd
to fix this issue, I also should rerunning
Hi Qian
if you just want to regenerate the pial, then yes, edit the
brain.finalsurfs.mgz and run:
recon-all -autrecon-pial -s -sd
note that it is NOT autorecon2-pial, but just autorecon-pial (leave out the
'2')
cheeers
Bruce
On Thu, 9 Feb 2017, 冉倩 wrote:
Hi Bruce,
If I use
Hi Bruce,
If I use brain.finalsurfs, then I run recon-all -autorecon2-pial -subjid sub01
or recon-all -autorecon2-pial -autorecon3 -subjid sub01? autorecon3 still need
rerunning? Thanks!
Best Regards,
Qian Ran
At 2017-02-08 12:19:35, "Bruce Fischl" wrote:
Dear Freesurfer developpers,
Is there a Freesurfer ColorLut that includes the new subfields of the
hippocampus ?
In the current colorlut there is no left/right for these subfields:
parasubiculum, GC-DG, HATA, molecular layer and tail. In addition, I think
it would be easier if the correct
Dear Graham,
you could also try mrconvert of mrtrix3. This tool is very useful and has very
good support.
http://mrtrix.readthedocs.io/en/latest/reference/commands/mrconvert.html
community.mrtrix.org
Regards,
Antonin
Unfortunately I'm not allowed to share these files without direct IRB
Unfortunately I'm not allowed to share these files without direct IRB approval
(even if they are anonymized). I just tried on some Siemens TrioTim data with
the same results.
Graham
From: freesurfer-boun...@nmr.mgh.harvard.edu
Can you upload the dicoms so I can test it out? filedrop address below
On 02/08/2017 02:13 PM, Warner, Graham Cary wrote:
> The set I'm look at now was collected on a GE Signa HDxt.
>
> Graham
>
> *From:*
Sent this to the wrong list. Apologies.
Quentin Funk, PhD
Houston Methodist Research Institute
713-363-9003
From: Funk, Quentin
Sent: Wednesday, February 8, 2017 11:17 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: FNIRT all NaN's
Freesurfer experts,
I have
The set I'm look at now was collected on a GE Signa HDxt.
Graham
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yendiki, Anastasia
[ayend...@mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 2:09 PM
To:
I'm using a large dataset from mi2b2 which contains data from multiple
vendors/models collected at different hospitals in the partners network between
2003 and 2016. The data I tried running mri_convert on was acquired in 2011.
Graham
From:
What scanner(s) was it acquired on?
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Warner, Graham Cary
[gwar...@mgh.harvard.edu]
Sent: Wednesday, February 08, 2017 2:07 PM
To: Freesurfer support list
Subject:
Hi,
I used following command to extract LGI values from a set of subjects:
recon-all -s -localGI
Output stats is saved in lh.aparc_lgi.stats file. By default, its
calculating LGI values of 35 areas using *Desikan-Killiany Atlas *but I am
interested in calculating LGI values using Yeo atlas of
Old versions of mri_convert (before 6.0) used to output a default Siemens
gradient table - this was not read from the header of the dicom file itself.
The 6.0 version reads the table from the header, as long as it is a relatively
modern dicom file that has the table in a standard position in
I just tried it on a few and while it was able to generate the nii files it
failed to generate the bval/bvec files I'm looking for. Is it not typical
behavior for mri_convert to generate bval/bvec files for DTI runs or is this an
error?
Graham
From:
Shouldn't you post this to the FSL list?
On 02/08/2017 12:17 PM, Funk, Quentin wrote:
>
> Freesurfer experts,
>
>
> I have a few fractional anisotropy images linearly registered to an FA
> atlas. I'd like to run FNIRT on them with reference the FA Atlas, but
> when I do, the output is entirely
Hi Andrew
the brain.mgz is very aggressively filtered explicitly for cortex and
wipes away some subcortical boundaries (e.g. lateral thalamus).
cheers
Bruce
On Wed, 8
Feb 2017, Andrew Davis wrote:
Hello FreeSurfer Developers,
I have been using FreeSurfer for segmenting T1-weighted
Hei
Dette er en tekstfil i web diskusjonsforum. Det er mange som bruker
Freesurfer. Teksten dreier seg om ny lisensfil i samband med en ny versjon. Det
aktuelle mailen angår ikke meg. Jeg bruker gammel Freesurfer på jobben som ikke
trenger ny lisensfil.
Hilsen
Pål
Dr. philos. Pål G.
Hello FreeSurfer Developers,
I have been using FreeSurfer for segmenting T1-weighted images, and I have
a question related to using the two outputs norm.mgz and brain.mgz.
It is my understanding that, by default, FreeSurfer uses the norm.mgz
volume to do partial volume weighting when outputting
Freesurfer experts,
I have a few fractional anisotropy images linearly registered to an FA atlas.
I'd like to run FNIRT on them with reference the FA Atlas, but when I do, the
output is entirely NaNs.
I ran the program in verbose mode--and everything is NaN's. e.g.:
SSD = -nann = 0
alright. Thank you so much!
- Ursprüngliche Mail -
Von: "Douglas N Greve"
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 8. Februar 2017 17:45:38
Betreff: Re: [Freesurfer] extract area.pial stats
No. The program is from version 6 so it is expecting v6
No. The program is from version 6 so it is expecting v6 naming conventions
On 02/08/2017 11:38 AM, Clara Kühn wrote:
> Thank you, I think it worked. I've attached the file again.
> There was one error message in the terminal output though:
>
> atlas_icv (eTIV) = 1287829 mm^3(det: 1.512705 )
Thank you, I think it worked. I've attached the file again.
There was one error message in the terminal output though:
atlas_icv (eTIV) = 1287829 mm^3(det: 1.512705 )
/nobackup/etsch2/kids/prepost-61kids//ZF1K.base/mri/aseg.presurf.mgz doesn't
exist, using old naming conventions
Is that
try typing:
rehash
then run it again
On Wed, 8 Feb 2017, Clara Kühn wrote:
I'm so sorry, I don't know anything about programming...
I downloaded it, copied it into my SUBJECTS_DIR as mris_anatomical_stats-doug
and tried to run the whole thing again like this:
mris_anatomical_stats-doug -mgz
It either has to be in your path or you need to supply the full path when
running it, like this
$SUBJECTS_DIR/mris_anatomical_stats-doug
On 02/08/2017 11:27 AM, Clara Kühn wrote:
> I'm so sorry, I don't know anything about programming...
> I downloaded it, copied it into my SUBJECTS_DIR as
I'm so sorry, I don't know anything about programming...
I downloaded it, copied it into my SUBJECTS_DIR as mris_anatomical_stats-doug
and tried to run the whole thing again like this:
mris_anatomical_stats-doug -mgz -cortex
$SUBJECTS_DIR/ZF1K.base/label/lh.cortex.label -f
You don't need to open it. Just download it and put it in your path. You
may want to call it something slightly differnt so that you don't
confuse it with the v5.3 version
On 02/08/2017 10:53 AM, Clara Kühn wrote:
> thanks. What kind of format is it? How do I open it?
>
> Cheers
> Clara
>
>
This error suggests to me that you are mounting some external drive, or
docker container, or some mix of file systems incompatible with symlinks?
Try moving the subject to a local directory
On 02/08/2017 10:41 AM, Taylor Hilton wrote:
> This is the output: ln: failed to create symbolic link
thanks. What kind of format is it? How do I open it?
Cheers
Clara
- Ursprüngliche Mail -
Von: "Douglas N Greve"
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 8. Februar 2017 16:43:47
Betreff: Re: [Freesurfer] extract area.pial stats
Try this version
This is the output: ln: failed to create symbolic link 'lh.white.H': Operation
not supported
> On Feb 8, 2017, at 10:38 AM, Douglas N Greve
> wrote:
>
> can you run the commands below and tell me what happens?
>
> cd
Try this version (same as version 6)
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
On 02/08/2017 04:55 AM, Clara Kühn wrote:
> Hi Doug,
>
> thanks for your reply. I tried it out and attached the lh.aparc.pial.stats
> file for you to take a look at. As far as I can
that is bizarre. Can you upload
lh.area.mid to our file drop (see end of email)
On 02/08/2017 05:21 AM, Bunday, Karen wrote:
> Yes, that's it. It just back to the command line after that.
>
> What do you think the problem is?
>
> BW
> Karen
>
> Karen Bunday, PhD
> Research Associate
> Sobell
if you used the identity matrix then it is the first one
On 02/08/2017 08:43 AM, Seung-Goo KIM wrote:
> Thank you very much, Doug,
>
> One more question: so the sig have all T-test results of contrasts
> like [1 0 0 … 0], [0 1 0 ... 0], …, [0 0 0 … 1], right? or [1 -1/(N-1)
> -1/(N-1), …
can you run the commands below and tell me what happens?
cd /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf
ln -s lh.white.preaparc.H lh.white.H
On 02/08/2017 09:44 AM, Taylor Hilton wrote:
> Apologies, that was an old log, attaching the relevant one here.
>
>
>
>
>> On Feb 7,
Hi Graham – Have you tried mri_convert? The 6.0 version should be able to
extract diffusion gradient tables and b-value tables from most standard recent
dicoms.
a.y
From:
>
on behalf of "Warner, Graham
Hi all,
Can we get dcm2niix added to the system instance of fsl? It can't find it in
5.0.7 or 5.0.9 (please let me know if it is somewhere else and I'm just not
seeing it). I'm having problems generating .bval and .bvec files from certain
DTI datasets using dcm2nii and the NITRC guys told me I
Thank you very much, Doug,
One more question: so the sig have all T-test results of contrasts like [1 0 0
… 0], [0 1 0 ... 0], …, [0 0 0 … 1], right? or [1 -1/(N-1) -1/(N-1), …
-1/(N-1)] ?
Best,
--
Seung-Goo KIM
> On 2017-02-06, at 18:54, Douglas N Greve wrote:
>
Yes, that's it. It just back to the command line after that.
What do you think the problem is?
BW
Karen
Karen Bunday, PhD
Research Associate
Sobell Department of Motor Neuroscience and Movement Disorders
Institute of Neurology, University College London
-Original Message-
From:
Hi Doug,
thanks for your reply. I tried it out and attached the lh.aparc.pial.stats file
for you to take a look at. As far as I can tell it's still reporting the white
surface area. Or am I reading it wrong?
Cheers Clara
- Ursprüngliche Mail -
Von: "Douglas Greve"
?Hello FreeSurfer Developers,
I have done partial volume correction of PET data as described in PETSurfer
stream. Now, I want to extract a mean intensity value of my ROI for each
subject. This ROI is defined in the fsaverage space and saved as a label. What
would be the best way to do it?
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