Hello,
How can I get a fsfast contrast map projection on the subcortical surfaces? The
sig.nii for each hemisphere has a value per vertex structure, but the mni305
result is per voxel.
I used mri_vol2vol and mri_segstats to get statistics for each subcortical
structure, but I need a value per ve
Hello,
Is there a way to run mri_pretess on fsaverage? It has no mri/norm.mgz file.
I'm trying to create surface files for each subcortical structure using
mri_pretess, mri_tessellate and mris_smooth.
Thanks!
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Hey all,
I used mri_aparc2aseg to map the cortical labels from the laus250 parcellation.
Now I need to create a new lookup table, mainly for displaying the labels'
names in freeview.
How can I know what id each label gets in my new laus+aseg.mgz file?
Thanks,
Noam
___
;s
> pretty straightforward. # lines are comments, then it is
>
> cheers
> Bruce
On Fri, 30 Oct 2015, Peled, Noam wrote:
> Hey all,
> I used mri_aparc2aseg to map the cortical labels from the laus250
> parcellation.
> Now I need to create a new lookup table, mainly fo
Hello,
I've noticed that in tracula 5.2 there's also a path.pd.trk file in the output
directory.
How can I read this file? I would like to read the actual splines and not the
probabilistic distribution in path.pd.nii.gz.
Thanks,
Noam Peled
___
Freesurf
try:
> track = next(track_gen)
> except (StopIteration, TypeError):
> break
> tracks.append(track)
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Peled, Noam
[npe...@mgh.harvard.e
if you visualize them.
Best,
a.y
On Tue, 16 Feb 2016, Peled, Noam wrote:
> Hello,
> I've noticed that in tracula 5.2 there's also a path.pd.trk file in the
> output directory.
> How can I read this file? I would like to read the actual splines and not the
> prob
...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki
[ayend...@nmr.mgh.harvard.edu]
Sent: Monday, March 07, 2016 12:09 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] path.pd.trk format
Yes, native diffusion space.
On Mon, 7 Mar 2016, Peled, Noam wrote:
> Thanks!
> Do you in which space are the
;s in diffusion space, you don't need any transform.
On Mon, 7 Mar 2016, Peled, Noam wrote:
> So for plotting the fibers, like in freeview, should I just use the
> /dmri/xfms/diff2anatorig..mat or
> /dmri/xfms/diff2anat..mat transformation matrices?
>
Hey all,
I'm running preproc-sess, and getting the following error:
...
Reading in mov rest/tmp.bbregister.28405/template.nii
Reading in ref .../mri/brainmask.mgz
Reading in and applying refmask .../mri/aparc+aseg.mgz
Cannot allocate memory
I checked, and the aparc+aseg.mgz file is ok (I can read
Hey all,
When loading two T1 in freeview, one for a subject and one for fsaverage, and
switching between them, only the tkreg RAS coordinates changes while moving the
mouse, not the RAS.
Does it mean that the RAS in freeview is always in MNI305?
Thanks,
Noam
_
.html
Thanks,
Noam
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Peled, Noam
[npe...@mgh.harvard.edu]
Sent: Wednesday, March 08, 2017 9:27 AM
To: Freesurfer support list [freesurfer@nmr.mgh.harvard.edu]
Su
Hey all
I'm trying to morph the fsaverage flat patch (?h.cortex.patch.flat) to the
freesurfer sample subject, and getting the following error:
mri_surf2surf --srcsubject fsaverage --srcsurfval lh.cortex.patch.flat
--trgsubject sample --trgsurfval lh.cortex.patch.sample.flat --hemi lh
ERROR: coul
Dear freesurfer experts,
I would like to present invasive electrodes from different subjects in the same
template brain.
I thought about doing a volumetric registration (all the electrodes are depth)
using mri_cvs_register:
mri_cvs_register --mov {subject} --template {template} --outdir
$SUBJ
Hey David,
Have you managed to find a solution for that?
Best,
Noam
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Zhou, David Wei
Sent: Thursday, April 7, 2016 3:10:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Nonlinear CVS reg
list; Peled, Noam
Subject: Re: [Freesurfer] Skull as an Object
Hi Alex,
Noam Peled (npe...@mgh.harvard.edu<mailto:npe...@mgh.harvard.edu>) can help you
with this because he is using Blender in his MMVT. - Matti
On Jul 21, 2018, at 1:45 PM, Bruce Fischl
mailto:fis...@nmr.mgh.harvard.edu&g
I need to transfer one of our patient's electrodes locations (depth electrodes,
they aren't located on the cortical surface) to MNI305 space.
For that, I'm trying to use mri_cvs_register to register the patient to
fsaverage. I'm using to the following command:
mri_cvs_register --mov subjid --te
t CVS template)"
Lilla
On Wed, 1 Aug 2018, Peled, Noam wrote:
>
> I need to transfer one of our patient's electrodes locations (depth
> electrodes, they aren't located on the cortical surface) to MNI305 space.
> For that, I'm trying to use mri_cvs_register to register t
mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Wednesday, August 1, 2018 11:19:16 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_cvs_register using fsaverage
FYI, fsaverage is already in MNI305 space
On 08/01/2018 11:14 AM, Peled, Noam wrote:
>
> Thanks Lilla!
>
; "Use the CVS atlas in MNI152 space as a target for registration (as
> opposed to the default CVS template)"
>
> Lilla
>
> On Wed, 1 Aug 2018, Peled, Noam wrote:
>
> >
> > I need to transfer one of our patient's electrodes locations (depth
> >
52.txt
against cvs_avg35_inMNI152/mri/brainmask.mgz, at least half of them were
outside the brain.
Any ideas?
Thanks,
Noam
____
From: Peled, Noam
Sent: Saturday, August 18, 2018 3:08:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_cvs_register using fsa
d.edu/pipermail/freesurfer/2018-January/055460.html
Lilla
On Sat, 18 Aug 2018, Peled, Noam wrote:
>
> It doesn't seem to work
>
> Here are the commands I was using:
>
>
> mri_cvs_register --mov $SUBJECT --mni --outdir
> $SUBJECTS_DIR/$SUBJECT/mri_cvs_register_to_mni --noc
Hey all,
I'm trying to morph patients' invasive electrodes into a template brain.
I'm not sure why, but sometimes, the applyMorph gives me the (1 1
1) coordinates for a subset of the electrodes, where the rest are ok.
In the output, for those electrodes I can see it writes "not valid",
electrodes_morph_to_colin27.txt or is it the terminal output?
Lilla
On Thu, 7 Feb 2019, Peled, Noam wrote:
> Hey all,
> I'm trying to morph patients' invasive electrodes into a template brain.
> I'm not sure why, but sometimes, the applyMorph gives me the (1 1
> 1)
G122/electrodes/electrodes_morph_to_colin27.txt
a
Am I missing something?
Thanks,
Noam
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Peled, Noam
Sent: Thursday, February 7, 2019 10:36 AM
To: Lilla Zollei; Freesurfer support list
Subject: Re: [Freesur
is
freesurfer-linux-centos6_x86_64-dev-20180622-7758bad
(hmmm, should I be worried it ends with 'bad'?)
Can it cause these kinds of problems?
From: Lilla Zollei
Sent: Thursday, February 7, 2019 2:04 PM
To: Peled, Noam
Cc: Freesurfer support list
Subject: Re: [Frees
Dear group,
I ran recon-all on a T1 nii file, which is in LAS orientation. The brain.mgz
turn out to be in LIA orientation.
I've tried to convert the nii file to RAS (mri_convert --in_orientation LAS
--out_orientation RAS ...), and rerun recon-all, but it didn't change the
results.
How do I make
, why not just run
recon-all, then mri_conver to whatever orientation you want?
Internally we have a consistent orientation that you can't easily change
cheers
Bruce
On
Sat, 9 Mar 2019, Peled, Noam wrote:
> Dear group,
> I ran recon-all on a T1 nii file, which is in LAS orientation.
Dear group,
How can I apply the talairach.m3z transformation on a list of points?
I was trying to use applyMorph on one of my subjects:
applyMorph --template $SUBJECTS_DIR/M1/mri/orig.mgz --transform
$SUBJECTS_DIR/M1/mri/transforms/talairach.m3z point_list
$SUBJECTS_DIR/M1/electrodes/electrodes_t
Dear group,
When trying to run mri_pretess, I'm getting this error:
znzTAGskip: tag=809120822, failed to calloc 1802706944 bytes!
Cannot allocate memory
Here is the full command I'm using (in the Martinos center, using ver6 stable):
mri_pretess /autofs/space/thibault_001/users/npeled/subjects/mg
Hello,
After running recon-all on a patient, the resulting T1.mgz coordinates system
turned to be LIA. Can I guarantee the recon-all output will be in RAS?
I also would like to run FS-FAST on this patient's fMRI task dataset, which is
in LSA.
Any recommendation what should I do to make sure both
(and right is right)? If so,
the answer is yes.
On 5/4/2020 12:50 PM, Peled, Noam wrote:
Hello,
After running recon-all on a patient, the resulting T1.mgz coordinates system
turned to be LIA. Can I guarantee the recon-all output will be in RAS?
I also would like to run FS-FAST on this patient&#
FreeSurfer? Sometimes the data
will go through several conversions and formats before analysis. If the
orientation info was lost or changed, then that could explain it
On 5/4/2020 1:22 PM, Peled, Noam wrote:
Thanks Doug!
Good to know that.
I realized I had a problem when I got activation on the wrong s
dicom to nii?
On 5/4/2020 1:56 PM, Peled, Noam wrote:
We are running a pilot, to try to analyze their epileptic monitoring unit
datasets using the Martinos tools (FreeSurfer and MNE)
The analysis was on an fMRI nii file, which I checked before running fsFast,
and it was LSA.
I wouldn't su
sed a left-right reversal.
On 5/4/2020 3:25 PM, Peled, Noam wrote:
They are using dcm2niix of MRIcroGL
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
On Behalf Of Douglas N. Greve
Sent: Mond
Dear FreeSurfer experts!
We are running FsFast pipeline to analysis our language task for epilepsy
patients.
Usually we are using FreeSurfer 5.3. We want to use a newer version, so I
decided to jump right to 7.1 (dev)
When trying to run
preproc-sess -surface {trg_subject} lhrh -s {subject} -fwhm
@nmr.mgh.harvard.edu
Cc: Peled, Noam
Subject: Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1
External Email - Use Caution
Hello Noam,
The python script /usr/local/freesurfer/dev/bin/slicedelay needs to be run with
a version of python that is 2.X, i.e.,
$ file /usr/local/freesurfer/dev
-rwxrwxr-x 1 rd521 rd521 4951 Oct 30 04:45
/usr/local/freesurfer/dev/bin/slicedelay
Thanks!
From: Greve, Douglas N.,Ph.D.
Sent: Friday, October 30, 2020 10:38 AM
To: Peled, Noam ; Freesurfer support list
Cc: Gumenyuk, Valentina ; Stufflebeam, Steven M.
; Douglas N Greve
Subject: Re
Thanks,
In my system, I aliased the python command to a local anaconda python3.8.
So to be able to use slicedelay, should I first alias python to python2?
Thanks,
Noam
From: fsbuild
Sent: Friday, October 30, 2020 2:37 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Peled, Noam
Subject: Re
Dear FreeSurfer community,
I encountered a recon-all error where I couldn't find on the web.
The error message is: "error: MatrixMultiply: m1 is null!". You can find the
complete log attached.
I used the stable7.1.1 version.
Thanks,
Noam
recon-all.log
Description: recon-all.log
alf of "Peled, Noam"
mailto:npe...@mgh.harvard.edu>>
Reply-To: FS Help
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, November 24, 2020 at 10:10 PM
To: FS Help
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] error: MatrixMultiply: m1 is null
Dear Fre
Hello all,
Can I use the -ss flag in freeview to save more than one figure?
Currently, I'm calling freeiew 3 times, each time with a different viewport
(sagittal, coronal, and axial)
Thanks,
Noam
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.e
of command lines in a text file like this:
freeview foo.mgz -viewport x -ss pic1.jpg
-viewport y -ss pic2.jpg
-viewport z -ss pic3.jpg
Then run:
freeview -cmd foo.txt
Ruopeng
On Jan 26, 2021, at 1:18 PM, Peled, Noam
mailto:npe...@mgh.harvard.edu>> wrote:
Hello all,
Can I use the -ss f
Hello,
I was running recon-all on a raw T1 image with the following properties:
dimensions: 126 x 144 x 88
voxel sizes: 1.78, 1.78, 1.78
Orientation: PSL
Besides the raw T1, I have other nii files with the same dimensions and
orientation that I want to visualize on top of the recon-al
Dear group,
I have preop and postop MRI scans of an epileptic patient.
I ran recon-all on the preop, and bbregister on the postop to register it to
the preop.
I'm not sure why, but the results weren't really good.
Maybe I should try using the longitudinal pipeline?
Thanks,
Noam
__
e specific that "weren't really good"?
On 5/6/2021 12:03 PM, Peled, Noam wrote:
Dear group,
I have preop and postop MRI scans of an epileptic patient.
I ran recon-all on the preop, and bbregister on the postop to register it to
the preop.
I'm not sure why, but the results weren
Hello!
I'm trying to use freeview to visualize FSPGR dicoms files.
I'm using ubuntu 18.04 with tcsh shell. I'm getting the following error:
sh: 1: Syntax error: Bad fd number
Here is the full error message:
Starting DICOMRead2()
dcmfile =~/Desktop/04254335/05641194
dcmdir = ~/Desktop/04
number
What if you use mri_convert to convert them to a mgz or nii volume? Do you get
the same error?
Ruopeng
On Sep 1, 2021, at 10:52 AM, Peled, Noam
mailto:npe...@mgh.harvard.edu>> wrote:
Hello!
I’m trying to use freeview to visualize FSPGR dicoms files.
I’m using ubuntu 18.04 with tcsh
...@nmr.mgh.harvard.edu
On Behalf Of Wang, Ruopeng
Sent: Thursday, September 2, 2021 10:00 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number
Would it be possible to send me the dicom files?
Ruopeng
On Sep 1, 2021, at 1:14 PM, Peled, Noam
>>
on behalf of Peled, Noam
mailto:npe...@mgh.harvard.edu>>
Sent: Thursday, September 2, 2021 12:19 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] freeview: sh: 1: Syntax error: Bad fd number
Unfortunately, it's patient data
2niix internally.
On 9/7/2021 5:11 PM, Fischl, Bruce wrote:
Our dicom reader is probably too old
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
On Behalf Of Peled, Noam
Sent: Tuesday,
your build: build-stamp.txt:
freesurfer-linux-ubuntu18_x86_64-dev-20210824-e101185
On 11/16/2021 4:26 PM, Peled, Noam wrote:
Dear Freesurfer group,
I was running recon-all (Freesurfer 7.2 on Ubuntu) and received the following
error:
“
mris_fix_topology -mgz -sphere qsphere.nofix
r-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Peled, Noam
Sent: Thursday, November 18, 2021 9:05 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all reconbatchjobs Segmentation fault
Thanks Doug!
Unfortunately, removing the paralle
d and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
> On 01/14/2022 5:02 PM Peled, Noam wrote:
>
>
> Dear group
> A colleague of mine was trying to run recon-all on one of her patients and
Hello,
I was running recon-all where SUBJECTS_DIR is
/space/megraid/clinical/MEG-MRI/seder/freesurfer, where we store our patient's
Freesurfer reconstructions.
I received the following error:
ERROR: Label FG1.mpm.vpnl does not exist in SUBJECTS_DIR fsaverage!
The fsaverage link probably po
allel? It looks like it is waiting for
some other PID to finish
Bruce
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Peled, Noam
Sent: Thursday, February 24, 2022 12:36 PM
To: F
"
I think the cerebellum and the dura seem to be ok:
[cid:image001.png@01D82A5B.F7813420]
Any ideas?
Thanks!
Noam
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Peled, Noam
Sent: Thursday, February 24, 2022 1:18 PM
To: Freesurfer support list
Subject: Re: [Freesurf
Dear group,
I have 2 images (preop t1 and postop CT), and a 4x4 registration matrix (as a
text file).
Is there an easy way to create an lta or xfm file to use it with mri_vol2vol?
Thanks!
Noam
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Freesurfer@nmr.mgh.harvard.edu
Dear group,
I'm trying to run Freesurfer on digitalOcean server running Ubuntu 22.10
(GNU/Linux 5.19.0-46-generic x86_64)
I Downloaded freesurfer 7.4.0
(freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)
After sourcing Freesurfer, recon-all gives following error:
.../freesurfer/bin/recon-al
sions?
2. use ‘chmod +x $FREESURFER_HOME/bin/recon-all’ to grant the permission
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all cannot ex
esurfer support list
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found
I’m wondering how you ran recon-all. Do you see the error even running it w/o
any arguments?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19,
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