Dear FreeSurfer Developers
Using "mris_volume surface_file_name " now i can't see any output files and
381271.851642 is shown in the command terminal, i have no idea what the
problem is. Could you please help?
Thank you!
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Does it give the exact volume ( the volume which the surface was made
from) or it gives an approximation of the volume? ( the toolboxes I've
already worked with for such a purpose; give poor approximations).
Thank you!
On Tue, Sep 19, 2017 at 6:40 PM Bruce Fischl
wrote:
> Hi Fereshte
>
> mris_v
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
Hi Andrew,
Thank you!
Here is the output of bugr
> [gschwind@login1 ~]$ bugr
> Cut-and-paste the following info into your FreeSurfer problem report:
> -
> FREESURFER_HOME: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64
> Bui
Dear Freesurfer Experts,
My apologies if I missed this information elsewhere on the website, but could
not find any info. about it.
There appear to be two Freeview versions, both from 2017 (released one day
apart), for which the screenshots are attached. I was wondering if you could
let me kno
Hi Markus, okay - I'll directly send you a tar of the vtk library. A reinstall
of vtk might work, because those shared objects that we distribute are usually
sym-linked
Can you also send the fs buildstamp? You can get this by running the command
‘bugr’ after sourcing freesurfer
Andrew
On Sep
fscalc, which is a general math program for volumes
On 09/19/2017 12:34 PM, std...@virgilio.it wrote:
> Thanks
> which is the command line for computation of (cesvar1+cesvar2)/2?
>
>
>> Messaggio originale
>> Da: "Douglas Greve"
>> Data: 19-set-2017 17.25
>> A:
>> Ogg: Re: [Freesurfer]
Thanks
which is the command line for computation of (cesvar1+cesvar2)/2?
>Messaggio originale
>Da: "Douglas Greve"
>Data: 19-set-2017 17.25
>A:
>Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: FS-FAST longitudinal analyis
>
>Don't do the subtraction on cesvar. Instead compute cesvar =
>(ces
try this one
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_convert.v53
On 09/19/2017 12:12 PM, Jyothirmayi Vadlamudi wrote:
> >From what I understand while going through, previous archives, a patch for
> >mri_convert will do.
> Unless there is another way to solve the problem with mri_c
>From what I understand while going through, previous archives, a patch for
>mri_convert will do.
Unless there is another way to solve the problem with mri_convert.
Date: Tue, 19 Sep 2017 11:28:52 -0400
From: Douglas Greve
Subject: Re: [Freesurfer] Error: nifti1Read(): unsupported slice
Hi Linnea,
I don't see any issue in the screenshots you sent. I couldn't find
freeview_T207_dtifit_FA.nii.gz.png in the attachment, either. Also your
second screenshot is comparing FA image with a b0 image, which will look
somewhat inversed.
Best,
Ruopeng
On 09/19/2017 09:17 AM, Linnea Mari
which file do you need?
On 9/19/17 9:11 AM, Jyothirmayi Vadlamudi wrote:
Hello Freesurfer users,
I am trying to run recon -all basic pipeline on CentOS x86-64 -
Freesurfer v5.1.0 .
I face the similar error as reported earlier by other users.
/nifti1Read(): unsupported slice timing pattern
Don't do the subtraction on cesvar. Instead compute cesvar =
(cesvar1+cesvar2)/2
On 9/19/17 4:17 AM, std...@virgilio.it wrote:
> I have run
> 1)
> isxconcat-sess -sf sessid_LONG_tp1 -analysis fc.rhseed.surf.rh -contrast
> R_SEED -o LONG_tp1
> isxconcat-sess -sf sessid_LONG_tp2 -analysis fc.rhsee
yes
On 9/19/17 3:22 AM, std...@virgilio.it wrote:
> Thanks. In the point 2) the tp1.gz and tp2.nii,gz are the ces.nii.gz that are
> computed using isxconcat-sess?
>
>
>> Messaggio originale
>> Da: "Douglas N Greve"
>> Data: 18-set-2017 23.03
>> A:
>> Ogg: Re: [Freesurfer] R: Re: R: Re:
Dear Andrew,
after the System admin executed your proposed commands, it stays the same,
Freeview aborts.
Is there anything else we could try?
Thank you and best wishes,
Markus
2017-09-15 20:06 GMT+02:00 Hoopes, Andrew :
> Hm okay thanks - I’m curious what happens when you run:
>
> cd $FREESUR
Hi Fereshte
mris_volumes computes and prints the volume of the interior of a closed
surface (a single number). It does not fill the interior. For that, use
mris_fill
cheers
Bruce
On Tue, 19 Sep 2017, Fereshte wrote:
Dear Professor Bruce
I'm just trying to convert lh.pial surface to the vol
Realized in my tooling around I had flipped T1 and hippoSf in my command.
Here is how the adjustment needs to be made for:
quantifyHAsubregions.sh hippoSf -
leftVolFile="$resultsDirectory/$subjectName/mri/lh.${*prefix*}Volumes-${*suffix*}.v20.txt"
rightVolFile="$resultsDirectory/$subjectNam
Hello,
I found a small bug in recent dev version bin quantifyHAsubregions.sh:
leftVolFile="$resultsDirectory/$subjectName/mri/lh.${suffix}Volumes-${suffix}.v20.txt"
rightVolFile="$resultsDirectory/$subjectName/mri/rh.${suffix}Volumes-${suffix}.v20.txt"
Should say
leftVolFile="$resultsDirect
Hello Freesurfer users,
I am trying to run recon -all basic pipeline on CentOS x86-64 - Freesurfer
v5.1.0 .
I face the similar error as reported earlier by other users.
nifti1Read(): unsupported slice timing pattern 5
In the previous archives, there are links provided, which are currently not
Dear Professor Bruce
I'm just trying to convert lh.pial surface to the volume with the down
below command but the output doesn't make any sense ( lh.voulme contains
zero). Could you please help?
Mris_volume topo_defect_after/surf/rh.pial
Thank you!
On Tue, Sep 19, 2017 at 1:11 PM Fereshte
wrote:
I have run
1)
isxconcat-sess -sf sessid_LONG_tp1 -analysis fc.rhseed.surf.rh -contrast
R_SEED -o LONG_tp1
isxconcat-sess -sf sessid_LONG_tp2 -analysis fc.rhseed.surf.rh -contrast
R_SEED -o LONG_tp2
2)
fscalc /LONG_tp1/fc.rhseed.surf.rh/R_SEED/ces.nii.gz -sub/ LONG_tp2/fc.rhseed.
surf.rh/R_SEED/c
Thanks. In the point 2) the tp1.gz and tp2.nii,gz are the ces.nii.gz that are
computed using isxconcat-sess?
>Messaggio originale
>Da: "Douglas N Greve"
>Data: 18-set-2017 23.03
>A:
>Ogg: Re: [Freesurfer] R: Re: R: Re: FS-FAST longitudinal analyis
>
>oh, I see now. In fsfast, you would
I changed the FreeSurfer version to 6 and now i could find it.
Thank you!
Cheers
On Sat, Sep 16, 2017 at 9:21 PM Douglas Greve
wrote:
> Is it not in $FREESURFER_HOME/bin ? What version are you using?
>
> On 9/16/17 12:05 PM, Fereshte wrote:
>
> Well i did ask if it was possible to obtain the vol
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