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Hi FreeSurfer experts,
I preprocess my data with FreeSurfer v 6.
After it I ran developmental version of freesurfer to get the hippocampus
subfields ROI and volume.
I get the following output:
# Hippocampal subfield volumes as created by segmentHA_T1
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Hi FreeSurfer experts,
I ran developmental version of freesurfer to get the hippocampus subfields ROI
and volume. I can see in the hipposubfields.lh.T1.v21.stats and
lh.hippoSfVolumes-T1.v21.txt fils with separate information for the head and
tail vo
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Hi I ran the following command not the subject on HPC
module load matlab/r2013a
module load freesurfer/6.0.0
source $FREESURFER_HOME/SetUpFreeSurfer.sh
fixup_mni_paths
recon-all -all -no-isrunning -s /hpf/projects/glongoni/ADHD-200/$file -subjid
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Hi please see the log below.
I do not understand the cause of the failure.
[nqureshi@qlogin1 ~]$ recon-all -s /hpf/projects/glongoni/ADHD-200/rest.nii
-subject ADHD-1 -all -hippocampal-subfields-T1 -sd
/hpf/projects/glongoni/ADHD-200/ -no-isrunnin
I want to know which atlas is used by Freesurfer to calculate morphometric
stats and global measure of volume.
Specifically for the sub-cortical regions.
Thank you.
Best,
Naveed
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Hi,
How can I find the following information from the MRI volume data already
preprocessed with Freesurfer.
1. Echo time
2. Repetition time
3. Flip angle
Thank you.
Best Regards,
Muhammad Naveed Iqbal Qureshi
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Hi, I have changed the path for subject directory. It causes the
error.Following is my SetUpFreeSurfer.csh What mistake did I made in?
#!/bin/tcsh -ef
#
# SetUpFreeSurfer.csh
#
# This is a sample SetUpFreeSurfer.csh file.
# Edit as needed for your specific setup.
# The defaults should wor
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Best Regards,
Muhammad Naveed Iqbal Qureshi
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Can we apply recon-all on a group of subjects simultaneously?
My system has good enough processing power to preprocess 40 subjects at a time,
but I have to open 40 terminal windows for doing it now.
I need an efficient way to do it.
Any suggestions?
Best Regards,
Muhammad
Naveed Iqbal
Hi,
How can I execute recon-all on an incomplete preprocessed file in
freesurfer.
My Pc was accidently shut down during the process.
Thank you.
Best Regards
Naveed
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Hi Zeke,
I have fixed the problem by reinstalling the FreeSurfer.
Thank you.
Best Regards,
Muhammad
Naveed Iqbal Qureshi
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> Date: Tue, 13 Jan 2015 11:01:52 -0500
> From: zkauf...@nmr.mgh.harvard.edu
> To: mniqure.
Hi Zeke,
Please find the attached log file.
Thanks
Best Regards,
Muhammad
Naveed Iqbal Qureshi
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> Date: Mon, 12 Jan 2015 11:33:29 -0500
> From: zkauf...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvar
eesurfer
> or, via email, send a message with subject or body 'help' to
> freesurfer-requ...@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
> freesurfer-ow...@nmr.mgh.harvard.edu
>
> When replying, please edit your Subject line so
report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
[naveed-centos@localhost ~]$
Best Regards,
Muhammad
Naveed Iqbal Qureshi
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volume to visualize it
correctly in spm
can anyone help me
waiting for your replies
Thank you
Best Regards,
Muhammad
Naveed Iqbal Qureshi
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Dear Experts,
I need to know how can I convert the .thickness files into volume file that can
be opened in SPM and show the thickness of each voxel in the standard templete
of the brain.
Thank you
Best Regards,
Muhammad
Naveed Iqbal Qureshi
/CHR01/rh.brik...
AFNI BRIK write unsupported
ERROR: failure writing
/media/Freesurfer_Data/Processed/AFNI_format/CHR/CHR01/rh.brik
UN:/media>
Please let me help me to solve this problem
Thank you :)
Best Regards,
Muhammad
Naveed Iqbal Qure
Dear Community,
Is it possible to detect the scanning power (either 1.5 or 3 tesla) of MRI
acquisition machine from the dicom images, if we do not know about the scanner
properties?
Best Regards,
Muhammad
Naveed Iqbal Qureshi
Dear Experts,
Is it possible to process the FreeSurfer thickness files of T1-MRI data in SPM
for ANOVA testing?
Is there any way to convert Freesurfer thickness files to SPM readable format?
Waiting for a precise reply.
Thank you.
Best Regards,
Muhammad
Naveed Iqbal Qureshi
Dear Experts,
Is it possible to process the FreeSurfer thickness files of T1-MRI data in SPM
for ANOVA testing?
Waiting for a precise reply.
Thank you.
Best Regards,
Muhammad
Naveed Iqbal Qureshi
Ph.D. Candidate
Bio-Medical Signal & System Analysis Laboratory
Department of Med
Hello,
Any help how to make qdec.table.dat file will be highly appreciated.
Thanks
Best Regards,
Muhammad
Naveed Iqbal Qureshi
Ph.D. Candidate
Bio-Medical Signal & System Analysis Laboratory
Department of Medical System Engineering
Gwangju Institute of Sciences and Technology
rds,
Muhammad
Naveed Iqbal Qureshi
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Dear list membes,
Please guide me how to create the qdec.table.dat for my own mri data.
Thank you.
Best Regards,
Muhammad
Naveed Iqbal Qureshi
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Dear List members,
Please guide me about installing qdec on Ubuntu.
Best Regards,
Muhammad
Naveed Iqbal Qureshi
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software tool read this thickness as numeric value?
Thank you.
Best Regards,
Muhammad
Naveed Iqbal Qureshi
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Frees
Best Regards,
Muhammad
Naveed Iqbal Qureshi
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Hello,
I am unable to find the .tcshrc files. Where can I find it.
I am unable to follow this process as stated on the website.
Alternately, the resource file for the shell can be configured to source the
file automatically each time the shell is started. In the home directory of
the us
Dear Community,
I need to know how can I read the numeric cortical thickness values from
freesurfer processed files. (as there are too many in the surf folder)
Thank you.
Best Regards
Naveed
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s/sub02/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Please guide me how to rectify this error. I have used the same command for
another dataset and it was working perfectly fine.
Best Regards,
Muhammad
Naveed Iqbal Qureshi
Ph.D. Candida
re to source the standard environment.Kindly reply me as soon
as possible.Thank you
Best Regards,
Muhammad Naveed Iqbal Qureshi
BK21 Student
Graduate Research Assistant
Computer Vision and Multimedia Lab
Department of Computer Engineering
Chosun University
375, Seosuk-dong, Dong-gu, Gwangju
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