External Email - Use Caution
Dear list,
I would like to find a reasonably good mapping from Desiken-Killiani ROIs and
as many of the resting state networks as makes sense, e.g. salience, visual,
etc.
I have made a start using the network <> ROI mapping in the Conn Toolbox
b
ll the sources that map to a given
target). If it is the 2nd stage that is giving you problems, then you can turn
it off in mris_apply_reg with --nnf (stands for "nearest-neighbor-forward", vs
the default nnfr where r=reverse).
On 12/3/2021 8:41 AM, Krieger, Donald N. wrote:
Exte
it off in mris_apply_reg with --nnf (stands for "nearest-neighbor-forward", vs
the default nnfr where r=reverse).
On 12/3/2021 8:41 AM, Krieger, Donald N. wrote:
External Email - Use Caution
Dear Bruce, Doug, and everyone,
1. I am projecting labels from a subject’s la
External Email - Use Caution
Dear Bruce, Doug, and everyone,
1. I am projecting labels from a subject's labels onto the icosahedron and
note that the mapping is not one-to-one. Because of this, I cannot tell which
subject vertex maps to which icosahedron vertex which I need
>>
On Behalf Of Krieger, Donald N.
Sent: Wednesday, July 21, 2021 10:53 AM
To: 'freesurfer@nmr.mgh.harvard.edu'
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] shortest distance between two points along the gray/white
boundary
External Email - Use
External Email - Use Caution
Dear experts,
I would like to compute the shortest distance along the gray/white boundary
between two points on the boundary, i.e. between points with "white"
parcellation regions. The distance need not be guaranteed to be minimized and
the path nee
between the white and pial vertex with the same label as a
cortical thickness?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Krieger, Donald N.
Sent: Thursday, February 11, 2021 1:16 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] cortical thickness values for each point in a
s are surfaces not labels or
annotations. If you want to extract labels from the annotations you can use
mri_annotation2label
On 2/11/2021 12:55 PM, Krieger, Donald N. wrote:
External Email - Use Caution
Dear freesurfer group,
I wish to measure a cortical thickness value for each entry in a
External Email - Use Caution
Dear freesurfer group,
I wish to measure a cortical thickness value for each entry in a label file,
e.g. SubNo/wmparc/ctx-lh-lateraloccipital_1011.label .
Is there a function in the freesurfer distribution which includes this
capability?
Also, is the
ailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Monday, October 21, 2019 7:37 AM
To: 'freesurfer@nmr.mgh.harvard.edu'
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] tracula FA question - 2 cohorts/2 scanne
External Email - Use Caution
I have tracula runs on two cohorts whose imaging was obtained on different
scanners with slightly different beta's and other parameters.
Would the differences in the scanners and scanning parameters be expected to
produce large cohort-wide differences
External Email - Use Caution
Please pardon me for jumping in here.
I looks like recon-all -autorecon1 will do it, yes?
Best - Don
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Bruce Fischl
Sent: Wednesday, October 16, 2019 12:48 PM
To: Fr
:14 AM, "Krieger, Donald N."
mailto:krieg...@upmc.edu>> wrote:
External Email - Use Caution
I extract the streamlines for each tract from path.pd.trk to an ascii file and
then wish to transform the coordinates to RAS T1 coordinates in millimeters.
My results are not cor
External Email - Use Caution
I extract the streamlines for each tract from path.pd.trk to an ascii file and
then wish to transform the coordinates to RAS T1 coordinates in millimeters.
My results are not correct.
Here is the extraction command I'm using. Is this correct? Perhaps
External Email - Use Caution
Is there a 4x4 transformation somewhere to convert mni coordinates to RAS T1
coordinates,
I.e. something comparable to the transforms provided by mri_info -tkrscanner
Thanks - Don
___
Freesurfer mailing li
External Email - Use Caution
Dear Mustafa,
The Open Science Grid has freesurfer 5.3 and 6.0 installations and provides a
simple user interface to upload scans, run freesurfer on them using OSG
computing resources, and download the results. This facility was designed to
meet the
d.edu
On Behalf Of Krieger, Donald N.
Sent: Wednesday, August 22, 2018 8:35 PM
To: 'freesurfer@nmr.mgh.harvard.edu'
Subject: [Freesurfer] mri_label2label dependencies
External Email - Use Caution
Dear freesurfers,
I am using mri_label2label with -regmethod volume .
The only
External Email - Use Caution
Dear freesurfers,
I am using mri_label2label with -regmethod volume .
The only other switches I am using are minimal as you can see below.
The thing is that none of the freesurfer stuff is in the srcsubject's directory.
Why is there no error message?
:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 2:10:50 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question
Ok - I have that sum.
For the forceps major, it's
a.y
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 1:
pr 11, 2018 12:00 PM, "Krieger, Donald N."
mailto:krieg...@upmc.edu>> wrote:
Thanks for getting back, Anastasia.
I'm not suggesting that it should be done differently than it is.
I'm just trying to understand how the voxel values map to probability. That's
why I des
54 AM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] newbie trac-all -bedp question
This wouldn't work because these 18 tracts do not include all tracts in the
brain.
On Apr 11, 2018 11:19 AM, "Krieger, Donald N."
mailto:krieg...@u
ecause these 18 tracts do not include all tracts in the
brain.
On Apr 11, 2018 11:19 AM, "Krieger, Donald N."
mailto:krieg...@upmc.edu>> wrote:
I was thinking that for a single voxel, the total of the values assigned to the
voxel over all the tracts would have a maximum o
fer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 10:43:11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question
Great - thanks - that's
iles
Best,
a.y
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Wednesday, April 11, 2018 8:
nd, all is well:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#BEDPOSTX
Best,
a.y
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on beha
fer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Tuesday, April 10, 2018 1:15:05 PM
To: freesurfer
Subject: [Freesurfer] newbie trac-all -bedp question
I am getting the following output with error on th
I am getting the following output with error on this command:
trac-all -bedp -s HDFT1001 -i ep2d_diff_SliceAcc_b1k_64_768x768.23
INFO: SUBJECTS_DIR is
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
INFO: Diffusion root is
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/sub
a.
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
Sent: Thursday, February 15, 2018 10:18:21 AM
To: Freesurfer
et the info without
running it unfortunately.
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Krieger, Donald N. mailto:krieg...@upmc.edu>>
ed in
$FREESURFER_HOME/FreeSurferColorLUT.txt.
Hope this helps,
a.y
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Krieger, Donald N." mailto:krieg...@upmc.edu>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: We
Dear List,
I need a list of Freesurfer ROIs which are typical endpoints for each standard
pathway used in tracula.
I think this information is likely included in the default tracula atlas which
I have been unable to find although I do not need spatial coordinates but
rather just the list of ROI
Hi Julia,
I’m sure one of the Freesurfer experts will reply soon.
Perhaps this will be helpful though.
It looks like recon-all is failing to find you dicom images.
You might want to post the recon-all command sequence you are using for them.
The first thing to check is that you are providing the
It looks like -autrecon2 is misspelled.
It should be -autorecon2
I hope this is helpful.
Best regards,
Don
[Signature0001]
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text
From: freesurfer-boun...@nmr.mgh.harvard.edu
[
Whereever there are spaces in the pathname, add a "\" in front of the space and
try again, e.g. instead of:
tkregisterfv --mov
/Users/djsandoval/Desktop/Selwyn/M87127996-2016004/Baseline/PETCT/PET/PET BRAIN
TOF STATIC 2/2016004A/IM-0001-0001.dcm --reg
/Users/djsandoval/Desktop/Selwyn/M8712799
Pardon me for poking in here. I hope this is helpful.
It looks like the failure is on an lseek command which means the file isn't
there or was truncated, as Zeke suggests.
When you deploy your jobs to the cloud cluster, perhaps there's a directive
which can be tweaked to give you a bigger plaype
s
> moved, then you will need to perform a registration to get them aligned.
>
>
> On 11/11/2016 04:17 PM, Krieger, Donald N. wrote:
> > Thanks for getting back, Doug.
> > I understand - but if there are two scans, aren't there two scanner RAS's
> > since
nput scans
-tkr2scanner gives the transform that takes "tkregister RAS" and
converts it to scanner RAS. "tkregisterRAS" is the RAS system used by
surfaces (it, a vertex xyz is in tkregisterRAS). See
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 11/10/2016 09:3
If I run recon-all with both a T1 and a T2 scan and switch t2pial, does
mri_info -tkr2scanner give me the transform to the T1 scanner frame of
reference?
And if I run recon-all with many T1's , what does mri_info -tkr2scanner give me
then?
Thanks - Don
recon-all run
ps. The 5.3 version is pretty buggy, so I'd wait until 6.0 to test it out
On 8/30/16 10:12 AM, Krieger, Donald N. wrote:
Dear list:
What are the advantages of including a T2 scan when running recon-all -all ?
Which results can it effect and to what extent?
And how sensiti
Dear list:
What are the advantages of including a T2 scan when running recon-all -all ?
Which results can it effect and to what extent?
And how sensitive is freesurfer to artifacts in the T2 scan?
Is there a good reference for this/
Thanks and best - Don
Hi Dorsa,
ImageJ and the people on the ImageJ mailing list may be helpful in transforming
one of the standard output formats provided by freeview, e.g. nii, to a
standard input format provided by COMSOL.
Here's a useful link.
http://imagej.nih.gov/ij/list.html
HTH - Don
> -Original Mes
Hi Renata,
Is there a problem with the “-s” argument, i.e. the “/” in - s 20110815/
HTH - Don
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Vaz pandolfo,
Renata
Sent: Thursday, July 07, 2016 8:05 AM
To: freesurfer@nmr.mgh.harvard.edu
For those who are interested, we have deployed a crude dynamic monitor for
freesurfer jobs running on the Open Science Grid.
It can be viewed at
http://xd-login.opensciencegrid.org/scratch/donkri/fsurfPoll.html .
The display information is in addition to that which is currently accessible
via "f
Dear FreeSurfer community,
The Open Science Grid (http://www.opensciencegrid.org) is a federation of
university and laboratory HPC facilities which share computing capacity to
support science.
We have developed a command line tool "fsurf" you can use from your laptop or
desktop computer to subm
I can see the sub directories and the distributions via ftp.
Best - Don
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Wednesday, June 29, 2016 10:57 AM
> To: Freesurfer support list
It looks like things aren't quite linked up.
I can reach the server with ftp and I can see directory pub.
But there's no directory pub/dist .
Best - Don
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Bru
>
> Use this version of mri_binarize
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize
>
> but doing the other things you want is a real programming job
>
> doug
>
>
> On 03/01/2016 09:29 AM, Krieger, Donald N. wrote:
> >
> > Freesurfe
Freesurfer provides 34 ctx label volumes on each side of the brain with
adjacent wm labels.
The boundary between each ctx volume and the co-named adjacent wm volume is a
third "white" label.
I would like to extract a few pieces of information from the analogous boundary
between each wm volume an
Hi everyone,
I'm reposting this from 2 days ago.
Please excuse if someone responded and I missed it.
We have been able to establish that we are getting identical results when
running recon-all -all on the same scan on different machine for the following:
All .mgz files in directories mri, mri/or
We have been able to establish that we are getting identical results when
running recon-all -all on the same scan on different machine for the following:
All .mgz files in directories mri, mri/orig, and mri/transforms, by comparing
using mri_diff ...
All of the .label and .annot files in director
unding a given vertex?
>
> mris_expand probably
> On Sat, 13 Feb 2016, Krieger, Donald N. wrote:
>
> > Thanks for posting back about this, Bruce.
> > I am thinking about a different function which probably is not called
> > --dilate.
> > One specifies a surface, e.g. w
ach will be better if you truly want a circle (although of course if the
> surface is highly curved then the metric won't be quite right)
>
> cheers
> Bruce
> On Sat, 13 Feb 2016, Krieger, Donald N. wrote:
>
> >
> > Hi Martha,
> >
> >
> >
> >
Hi Martha,
A brute force but simple way to do this is to use the list of labels contained
in subjects/nnn/label/lh.cortex and rh.cortex.
Given a vertex x,y,z, go through the file and select the lines for which the
distance to x,y,z <= 2 mm. This will give you a bunch of labels for points
withi
mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Wednesday, February 10, 2016 8:15 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] difference in 001.mgz found
>
> yes, we store the command lines used to generate a .mgz in the header, so that
> makes sense Bruc
age-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Krieger, Donald N.
> Sent: Wednesday, February 10, 2016 6:38 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] comparing multiple runs on the same scan
that is
different. It should print a report to the terminal. Do they not give
the same results?
On 02/10/2016 04:36 PM, Krieger, Donald N. wrote:
> mri_diff finds no differences in the mri/orig/001.mgz's but the checksums are
> different.
> In fact, their sizes are
ff on it to see what the difference is?
>
> cheers
> Bruce
> On Wed, 10
> Feb 2016, Krieger, Donald N. wrote:
>
> >
> > We would like to confirm that we are getting identical results from
> > multiple freesurfer runs on the same data set.
> >
> > To do so we
) or mris_diff for surfaces to check
whether they are different.
[Image removed by sender.]
hth
d
On Wed, Feb 10, 2016 at 2:14 PM, Krieger, Donald N.
mailto:krieg...@upmc.edu>> wrote:
We would like to confirm that we are getting identical results from multiple
freesurfer runs on the same da
We would like to confirm that we are getting identical results from multiple
freesurfer runs on the same data set.
To do so we are comparing identically named files using md5sum and would very
much appreciate your thoughts on our results. For multiple files, we
concatenate them and pipe the out
Dear List,
I have run recon-all -all on the same scan on two different machines likely
running two different versions of Linux but in any case the runs were done with
different numbers of cores.
I haven't done anything fancy to compare that the results are identical except
for some spot checks
Dear List,
I have a visualization problem which is not directly relevant to freesurfer but
which may be easily solvable with the freesurfer tools.
I have also posted this question to the ImageJ discussion list.
I would like to visualize "spherical" cuts through an MR.
An axial cut is the interse
Hi Joost -
Here's my understanding which comes from limited experience with PBS and SLURM.
Your master process is a bash, tcsh, or other shell script with PBS directives
embedded in it.
Each recon-all command within your script should include a -openmp N switch
which specifies the number of the
fore
> rerunning
>
> cheers
> Bruce
> On Wed, 18 Nov 2015, Krieger, Donald N. wrote:
>
> >
> > I have run freesurfer 6Beta on the scan with very large CSF spaces
> >
> > With flags: -bigventricles and –notal-check .
> >
> > I used t
I have run freesurfer 6Beta on the scan with very large CSF spaces
With flags: -bigventricles and -notal-check .
I used the latter flag per suggestions in the log as the first run failed on a
talaraich check.
This second run appears to be hung as it has not written anything new into the
recon-all
see how it goes
cheers
Bruce
On Tue, 17 Nov 2015, Krieger, Donald N. wrote:
A few cuts from a grossly abnormal scan are attached.
Do you think freesurfer can effectively segment this one?
If so, please point us in the right direction to get started with it.
A few cuts from a grossly abnormal scan are attached.
Do you think freesurfer can effectively segment this one?
If so, please point us in the right direction to get started with it.
Thanks. - Don
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
This is a newbie question as this is the first grossly abnormal scan on which I
need to run freesurfer.
There are very large CSF spaces and only a rim of cortex and white matter for
many regions.
Freesurfer fails very early on.
Before I post errors, I would like to try to get it to complete if th
t: Re: [Freesurfer] list of normals to triangle vertices
>
> Hi Don
>
> 1. I think so, yes.
> 2. Yes.
> 3. The convention is that they point outwards from wm->ctx 4. Yes.
>
> On Tue, 13 Oct 2015, Krieger, Donald N. wrote:
>
> > Thanks very much, Bruce.
> >
]].z;
>d1 = -v1[1]*v0[2] + v0[1]*v1[2];
>d2 = v1[0]*v0[2] - v0[0]*v1[2];
>d3 = -v1[0]*v0[1] + v0[0]*v1[1];
>return sqrt(d1*d1+d2*d2+d3*d3)/2;
> }
>
>
>
> cheers
> Bruce
>
>
> On Tue, 13 Oct 2015, Krieger, Donald N. wrote:
>
> >
>
Hi everyone,
I need to create the vector normal to the surface at each "white" vertex.
I would like to end up with 7 fields in each entry:
1 Vertex number
2-4 RAS coordinates
5-7 RAS components of the normal vector pointed from ctx --> wm
mri_annotation2label gets me the first 4.
I just
5mm of
cortex or else it gets "Unsegmented White Matter". The method is described here
http://www.ncbi.nlm.nih.gov/pubmed/19027860
On 7/7/15 8:36 PM, Krieger, Donald N. wrote:
Freesurfer provides ctx- and wm- volumes on either side of the "white" labelled
sheet, all for a
Freesurfer provides ctx- and wm- volumes on either side of the "white" labelled
sheet, all for a particular cortical region.
What is the idea which is used to limit the extent of the wm- volume which is
adjacent to a particular ctx- volume?
Is it as simple as a maximum distance normal to the whi
t; ubuntu 14.04 crash with Illegal instruction (core dumped)
>
> I will make it available to you and send you a link on Tuesday.
>
> -Zeke
>
>
> > On May 23, 2015, at 10:48 AM, Krieger, Donald N.
> wrote:
> >
> > Hi Zeke,
> >
> > I would like to t
Hi Zeke,
I would like to try that version on comet to see if I get a significant
speed-up.
Can you provide an address and pathname from which I can use wget to grab it?
I'll report back with results compared with the standard release.
Thanks,
Don
Don Krieger, Ph.D.
Department of Neurological Su
o, it would be good to
> backup the version you currently have.
>
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/
>
> -Zeke
>
> On 05/01/2015 05:02 PM, Krieger, Donald N. wrote:
> > I have completed runs of recon-all -autorecon1 and recon-all
>
I have successful runs of recon-all -autorecon1 and recon-all
-autorecon2-volonly per your suggested sequence:
recon-all -s subj -autorecon1
recon-all -s subj -autorecon2-volonly
recon-all -s subj -autorecon2-perhemi -hemi rh -log recon-all-hemi rh.log
-notify rh-done.log -openmp 4 &
recon-all -s
Thanks very much for getting back so quickly.
The processing times were 5-6 hours for all instances.
There is an incremental but only modest improvement for 4/6 vs 8/12 processors.
I'll put up more information on the list when I've finished thinking this
through.
Regards,
Don
Don Krieger, Ph
I'm testing the total processing time of recon-all -all using -openmp 4,6,8,12 .
The runs with 4 and 6 threads took almost the same amount of time.
The runs with 8 and 12 threads took almost the same amount of time.
(1)Is the work divided evenly between the threads (mri_ca_register,
mri_en_re
> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
> Sent: Friday, March 13, 2015 11:01 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] follow up and double check: transform RAS vectors to
> talaraich
>
>
>
> On 3/13/15 10:10 AM, Krieger, Donald N. wrote:
&
are trying to do or what the
> mri_info command is related to. Can you fill in the details?
>
> On 03/12/2015 04:20 PM, Krieger, Donald N. wrote:
> > Do the results in the attached images make sense?
> > Does it make sense that the transformation was obtained: mri_info --vox2ra
hat do you want us to check?
>
> On 03/12/2015 03:27 PM, Krieger, Donald N. wrote:
> >
> > Dear List,
> >
> > I've done a couple of spot checks which appear to work but want to
> > double check with you.
> >
> > Attached are 5 axial cuts from fsavera
] On Behalf Of Krieger, Donald N.
Sent: Thursday, March 12, 2015 3:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] follow up and double check: transform RAS vectors to
talaraich
Dear List,
I've done a couple of spot checks which appear to work but want to double check
wit
ons: transform RAS vectors to talaraich
> vectors and view
>
>
> On 03/12/2015 09:54 AM, Krieger, Donald N. wrote:
> >
> > Dear List,
> >
> > I have sets of vectors in RAS coordinates from many volunteers.
> >
> > I want to transform them into coordinate
Dear List,
I have sets of vectors in RAS coordinates from many volunteers.
I want to transform them into coordinates for a standard volume.
(1) I presume the standard volume that makes sense to use is orig.mgz in
$FREESURFER_HOME/subjects/fsaverage/mri. Please confirm.
(2)I presume tha
Of Zachary Greenberg
Sent: Wednesday, March 04, 2015 7:47 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mris_convert lh.pial to lh.pial.asc coordinate shift
awesome! thanks a bunch Don.
-zack
On Wed, Mar 4, 2015 at 4:24 PM, Krieger, Donald N.
mailto:krieg...@upmc.edu>> wrote:
H
Hi Zack,
It looks like mris_info send that matrix out on the error output rather than
the standard output.
I just tried it and you can get it by redirecting both to your file like this:
Try mris_info lh.pial >& lh_info.txt
Regards,
Don
[Signature0001]
Don Krieger, Ph.D.
Department of Neurolog
Your environmental variables need to be set in the environment you use.
I don’t think the environment gets carried through when you use “sudo”.
That’s why your status messages show things like:
Working in SUBJECTS_DIR: /analise//
$SUBJECTS_DIR didn’t get interpreted.
You can double check by tr
ject dir
> and let
> us know
>
> good luck
> Bruce
>
>
> On
> Wed, 11 Feb 2015, Krieger, Donald N. wrote:
>
> > Thanks for responding so quickly, Bruce.
> > Yes I was running a single job on the 6-core machine and have used it and
> this version of r
g a single job on the 8G machine? What FS version? We haven't
> seen any core dumps in mri_ca_register recently. If you run it without openmp
> does it work? Kind of worrisome that it dies in a different place on a
> different
> machine Bruce
>
>
> On Wed, 11 Feb 2015, Kri
Dear list:
We are under a significant deadline on which this freesurfer run depends.
I'm reposting from last night along with a bit of additional information.
A 2nd run on a different box yielded:
nu_correct: crashed while running nu_estimate_np_and_em (termination
status=256)
Also, the box
Any help and direction you can provide with this error would be appreciated.
The full log is attached.
I was running with -openmp 5 on a machine with 6 cores and 8 Mbytes of RAM.
0033: dt=73.984000, rms=0.641 (0.133%), neg=0, invalid=96777
0034: dt=73.984000, rms=0.640 (0.104%), neg=0, invalid=967
Dear freesurfer team:
I just updated to Fedora 21 and freeview failed with errors finding
libpng12.so.0 and libXss.so.1 .
I copied these from an earlier version of Fedora into /usr/lib64 and freeview
now works.
I'm running recon-all under this new release and will post back if there are
proble
Muhammad,
I think your question is not so much a freesurfer one but more general.
You want to run 40 jobs in the background so terminals won't be needed once
they are spawned.
The way to do it is issue commands like this:
( cmds for job1; cmds for job2; ... ; cmds for jobM ) &
( cmds for jobM+1;
It looks like there's a typo in your recon-all command - there's a space
between "-" and autorecon3 .
Regards,
Don
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text
> -Original Message-
> From: freesurfer-bo
It looks like the ln -s command is failing either because dwi.nii.gz does not
exist or data.nii.gz does exist.
I think you've ruled out that you don't have write permission to the directory
by trying to execute it as root.
ln -sf /media/Sokol/Subj/041/dmri/dwi.nii.gz
/media/Sokol/Subj/041/dmri/
Dear Jens,
I can offer just a bit of information and I also have a question.
We are using Fedora 11.0 on an x86_64 box and both the Centos 4 and Centos 6
compiles work.
The package appears to be self-contained as I have seen no faults on failures
to find shared libraries.
We simply untar freesur
/pub/dist/freesurfer/freeview/linux_centos6_x86_64/freeview.bin>
> 86_64/freeview.bin<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/freeview.bin>
>
> and copy it to $FREESURFER_HOME/bin
> then
> chmod a+x $FREESURFER_HOME/bin/fre
I recently downloaded and installed
freesurfer-Linux-centos6_x86_64-table-pub-v5.3.0.tar.gz .
I had been running this version previously but had to reload everything due to
a disk crash.
recon-all -all goes to completion with no errors.
freeview starts up fine but fails on loading a volume file
c since it is a complete tiling of the
> surface. Each point is assigned the most likely label with no holes, so no
> thresholding is needed.
>
> cheers
> Bruce
> On Thu, 11 Sep 2014, Krieger, Donald N. wrote:
>
> >
> > Hi Anastasia or anyone,
> >
> >
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