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Dear HCP team ,
Could you please let me know how i can configure CUDA 9.1 with freesurfer
6.0 or Freesurfer 5.3.0 -HCP
It is taking a long time by using openmp to run recon-all.
please let me know if you have any suggestions for parallelization.
External Email - Use Caution
Dear all,
When i run recon-all , i am encountering an error transforms/ talairach.m3z
not found during registration phase, could some one please let me know how
to resolve this?.
Thanks
Vasudev
___
External Email - Use Caution
Dear all,
I am using - openmp 30 to run recon-all, i see now change in the execution
time period.
Could you please highlight me a method to reduce the execution time for
recon-all, if possible some parallel script to do that same.
Thanks
Vasudev
External Email - Use Caution
Dear all,
How can i create .annot files for both left and right hemisphere from nifti
atlases http://www.gin.cnrs.fr/en/tools/aal/
are there any specific guidelines or commands for surface based
parcellation ?
Thanks
Vasudev
source is now compiled with C++ compilers, and I don’t know that
> anyone has tried building with cuda since we changed the compilers for
> freesurfer.
>
> - R.
>
> On Aug 30, 2019, at 11:39, Dev vasu
> wrote:
>
> External Email - Use Caution
>
> Dear all,
>
&
External Email - Use Caution
Dear all,
Does recon_all -use-gpu only works for CUDA 5.0, is there any way to make
it work for CUDA 9.1.
Thanks
Vasudev
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Freesurfer@nmr.mgh.harvard.edu
External Email - Use Caution
Dear all,
I am having a difficulty in transforming the segmented subfields of
Amygdala atlas from surface based .mgz to nifti format.
I have extracted the labels using mri_extract_label
lh.hippoAmygLabels-T1.v21.nii.gz 7009 Cortico_amygloid.mgz
then
External Email - Use Caution
Dear all,
I am having a difficulty in transforming the segmented subfields of
Amygdala atlas from surface based .mgz to nifti format.
I have extracted the labels using mri_extract_label
lh.hippoAmygLabels-T1.v21.nii.gz 7009 Cortico_amygloid.mgz
then
External Email - Use Caution
Dear all,
I am trying to convert .mgz file to nii.gz using mri_convert command
mri_convert filename.mgz filename.nii.gz
but i am getting an error
"mri_convert: error while loading shared libraries: libGLdispatch.so.0:
cannot open shared object
External Email - Use Caution
Dear all,
I have used Freesurfer pipeline for Thalamic Nuclei segmentation, the
results of segmentation appear to be very poor, i am annexing the results ,
please kindly review if there is any thing wrong with the segmentation
results.
Thanks
External Email - Use Caution
Dear all,
I am encountering following error whenever i re-rerun my recon-all on
cluster,,although i have downloaded new development version of
recon-all.makefile, this error persists,kindly let me know what i am doing
wrong
recon-all -make all -s
External Email - Use Caution
Dear all,
I was trying to run recon-all, the pipeline terminated in middle now i
would like to know if there is any way i can restart it from the point
where it was terminated?.
Thanks
Vasudev
___
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Dear All,
I have a problem with the Freesurfer hippocampal longitudinal segmentation
results , when i have done segmentation using following algorithm (
https://github.com/CobraLab/antsRegistration-MAGeT) with no
anterior/posterior partitioning (
External Email - Use Caution
Dear All,
I have a problem with the Freesurfer hippocampal longitudinal segmentation
results , when i have done segmentation using following algorithm (
https://github.com/CobraLab/antsRegistration-MAGeT) with no
anterior/posterior partitioning (
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
> --
> *From:* Dev vasu
> *Sent:* Tuesday, July 3, 2018 12:22:27 AM
> *To:* Iglesias Gonzalez, Eugenio
> *Cc:* freesurfer@nmr.mgh.harvard.edu
>
> *Subject:* Re: Anterior /
External Email - Use Caution
Dear Sir,
I have another query if i use "export WRITE_POSTERIORS=1", will it generate
posterior CA1 and other substructures in the form as cited
*posterior_sidev2x.mgz
, *
Thanks
Vasudev
On Mon, Jul 2, 2018 at 8:30 PM
gt;
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: *Dev vasu
> *Date: *Monday, 2 July 2018
(CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: *Dev vasu
> *Date: *Monday, 2 July 2018 at 17:09
> *To: *"freesurfer@nmr.mgh.harvard.edu" , "
> igles...@nmr.mgh.harvard.edu&q
External Email - Use Caution
Dear Sir,
I have reviewed your journal which detailed about hippocampus parcellation
(
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
) of subfields ( HBT - Head/body/Tail) , could you please let me know how
to
Dear all,
I have custom ROI mask ( MNI Space ) that i have prepared from Jülich
atlas , I would be like to obtain corresponding surface label file, Could
you please guide me necessary the steps that i have to follow inorder to
obtain corresponding label for my mask.
Thanks
Vasudev
Dear all,
I have a ROI mask volume file and i would like to generate Mean cortical
thickness surface file (i.e lh.ROI.thickness.fsaverage.mgh and
rh.ROI.thickness.fsaverage.mgh) , could some one guide me how i could
obtain such file.
I have 120 subjects and I have done recon-all for all
Dear Sir,
I have performed Subfield segmentation of Hippocampus subfields, I would
like to how i can calculate thickness of each subfield post segmentation,
are the values in the text files
*[lr]h.hippoSfVolumes--.v10.txt*: indicate estimated
volume of each subfield , Is there any way i can
Dear all,
I am encountering following error when i run Hippocampus subfield
segmentation
"run_segmentSubjectT1_autoEstimateAlveusML.sh: line 46: 11266
Aborted "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML
$args ".
I am annexing the log file for your notice please kindly
Dear all,
I have 115 subjects , and I would like to perform average cortical
thickness ,pial surface .
I have used mri_concat for this and i am getting dimension mismatch
*" mri_concat k***/surf/lh.thickness --mean --o
Dear all,
I would like to if there is any procedure to reorient the image ( flip )
from AP axis to PA , I have around 50 scans all of which are scanned in A/P
axis and i would like to reorient them , kindly please let me know if there
is any procedure.
I tried mri_convert and orient_mri is
Dear all ,
I have been incurring lot of problems while running recon-all on ubuntu
16.04 , recon-all throws following error :
" #@# Curv .H and .K lh Sa 25. Feb 04:09:16 CET 2017
/media/vasudev/vkirsch4/Project_BLVP/HCP_Proj/KON2/T1w/KON2/surf
mris_curvature -w lh.white.preaparc
total
Dear FreeSurfer Developers,
I am incurring Talairach registration error when i was running recon-all -s
Error :
recon-all -s KON2 exited with ERRORS at Do 16. Feb 16:23:10 CET 2017
Freesurfer Version : freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP
Platform: Ubuntu 16.04
recon-all log
Dear all,
I would like to perform Group ROI analysis between healthy controls and BVF
patients where i would like measure cortical thickness changes between
healthy controls and BVF, what changes should i adopt to my initial
preprocessing tasks using recon-all in order to evaluate changes in
Dear all,
Is there any approach that you recommend to quantify that changes in
cortical thickness in hippo campus sub fields , how could i perform
Surface based cortical thickness changes using freesurfer.
Thanks
Vasudev
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Dear all,
Could you please suggest me some method where i can possibly convert
Wavefront .obj files into Nifti files, is such conversion technically
relevant ?.
Thanks
Vasudev
___
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Freesurfer@nmr.mgh.harvard.edu
Dear Freesurfer Group,
I would like to perform group analysis for 50 Subjects (25 healthy controls
and 25 Subjects with BLVP ) and examine the changes in cortical thickness
between 2 groups, could you please kindly inform me some methods that i
should adapt to perform the analysis.
Thanks
Dear all,
I would like to like obtain the data values of IntraCranial Volume (ICV)
for 10 subjects , i know that recon-all automatically calls mri_segstats,
but i would like to know if there is any other method to obtain ICV
quickly, since running recon-all on each subject takes a lot of time.
Dear all,
I would like to like obtain the data values of IntraCranial Volume (ICV)
for 10 subjects , i know that recon-all automatically calls mri_segstats,
but i would like to know if there is any other method to obtain ICV
quickly, since running recon-all on each subject takes a lot of time.
Dear Sir / madam,
I have tried running recon-all with GNU parallel and i am incurring
following error kindly review the recon-all.log ( see below ).
Could you please let me know why such problem persists for me. Is it the
issue with memory space ?
Thanks
Vasudev
Calling the GNU parallel in
Dear Sir / madam,
I have tried running recon-all with GNU parallel and i am incurring
following error kindly review the recon-all.log ( see below ).
Could you please let me know why such problem persists for me. Is it the
issue with memory space ?
Thanks
Vasudev
Calling the GNU parallel in
Dear sir,
I was checking for your reply about my question in Freesurfer Forum but
unfortunately i could not your answer although ":Freesurfer Digest, Vol
150, Issue 43 " Today's topics section indicates that you have replied to
my question.
Following is my question :
In order to run my
Dear Sir,
In order to run my structural analysis pipeline , i require T2w images,
but unfortunately we have not performed T2w scans , my colleague suggests
we can use rfMRI instead T2w images Could you please let me know if i can
use rfMRI image instead of T2w image?.
Thanks
Vasudev
Dear all,
After running through recon-all ,I have obtained wmparc parcellation file
(see the attached figure ). I would like to obtain parcellation at specific
regions of interest for my study i.e Brain stem region and Thalamus
region, could you please let me know how i could perform
Dear sir,
I would like to know how could i possibly generate white and pial surface
data for pool of 50 subjects ( 25 healthy controls and 2 subjects with
BLVP) using free surfer.
Thanks
Vasudev
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Dear Sir / madam,
I have 50 subjects (25 healthy controls and 25 patients with BLVP) , I
would like to know how could i generate cortical thickness maps for multi
subject group analysis.
The initial pre-processing with recon-all takes several hours for single
subject, is there any alternate way
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