Hi list,
I'm configuring mkanalysis-sess to configure an analysis for FC data by
FS-FAST. I do not understand how I can perform mni305 volume-based analysis.
How can I configure an analysis for mni305? Specifically, which is the paradigm
file in
-taskreg? How is the command for group level prep
Hi Xiaofu - As I said earlier, it is impossible for us to troubleshoot
problems with every single type of cluster, especially a type we don't
have. You'll have to troubleshoot it with your cluster admin, or try to
run bedpostx on a stand-alone computer. About your other questions:
1. Current
Dear Anastasia,
Thanks for your answer. I tried to replace 'bedpostx_mgh' with 'bedpostx'
in the shell file 'tract-all' in order to run Tracula in the C2B2 server
(Titan cluster). But it failed as well. Is there anyway to run Tracula,
i.e., by pass the running error of bedpostx_mgh?
Besides, I
Sorry, I thought my original post would be somehow linked to the second
one. Here it is:
Dear Freesurfer experts,
I would like to segment a WM skeleton I derived using FSL's TBSS into ROIs
based on white matter regions as derived in the wmparc.mgz file. I thought of
using the "fsaverage" subject
Hello freesurfers,
I am once again trying to run ex-vivos brains on freesurfer, with a new set
of data.
I am using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 on a Intel®
Core™ i7-2630QM CPU @ 2.00GHz × 8 running ubuntu 14.10 64-bit
I was following the ex vivo suggested protocol (
http://f
Hello Freesurfer team,
When generating the .stats files for grey matter volumetric data, this
information appears in multiple places and I'm not sure which data I should be
using for my final results.
There appears to be cortical information generated in both the .stats file
based off the DK
Hello Freesurfer
mni152reg --s 0201JB-anat
=> mkdir: cannot create directory
`/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.31253':
Permission denied.
Thus I put this command following the way of searching freesurfer mail support.
chmod ugo+w /usr/pubsw/packages/fsl/current/dat
what is the question?
On 05/26/2015 12:55 PM, Estephan J. Moana-Filho wrote:
> Any suggestions? I've perused the freesurfer mailing list and couldn't
> find any advice specifically to this question.
>
> Estephan
> ___
> Freesurfer mailing list
> Freesurf
Hi Melissa, please send responses to the list. Thanks! Yes, this is
possible. You'll need to analyze each of your subjects in FreeSurfer
with recon-all, QC them, then run mris_preproc, mri_surfsurf to smooth,
then mri_glmfit and mri_glmfit-sim. See the tutorials that we have on
our wiki.
doug
Hi Melissa, what is MACACC analysis?
doug
On 05/26/2015 12:42 PM, Melissa Levesque, Ms. wrote:
> Hi all,
> I'm used to getting cortical thickness/surface area/volume values using CIVET
> and minc-tools and I am trying to learn/convert to freesurfer tools. I want
> to perform a MACACC analysis. C
Any suggestions? I've perused the freesurfer mailing list and couldn't
find any advice specifically to this question.
Estephan
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The
Hi all,
I'm used to getting cortical thickness/surface area/volume values using CIVET
and minc-tools and I am trying to learn/convert to freesurfer tools. I want to
perform a MACACC analysis. Can anyone recommend some good documentation about
making the switch to freesurfer or which specific too
Hi Anthony
sorry, I know you've posted this before. What version are you running?
And what type is your labeled data? That is, are they uchar? int? At some
point this used to not work with non-uchar data, but I think I fixed it a
while ago. YOu might try downloading a beta of V6 and see if it f
Hello,
I have been stumped by this error I keep getting using the
rebuild_gca_atlas.csh script. I am trying to build a cerebellar atlas,
so I am wondering if the problem is with the brains we parcellated, or
with my installation etc. The brains consist of manually segmented
cerebellums from the o
The error is "ERROR: reading ./rh.unknown.label" meaning that it is
expecting it as input. You need to create it or change the command to
not expect it
On 05/26/2015 08:32 AM, Liu Y wrote:
> no ./rh.unknown.label was created.
> Yawu
>
> On Mon, May 25, 2015 at 7:22 PM, Douglas Greve
> mailto:
the surface-based stats file are produced by mris_anatomical_stats, the
volume-based stats files are produced by mri_segstats. Not sure about
your question
doug
On 05/26/2015 07:16 AM, Hassan bakhshi wrote:
> Hi,
>
> I wanted to ask what is the difference between stat files result and
> the mri
Please see
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On 05/26/2015 03:24 AM, Sofia Rodriguez Penuela wrote:
>
> Dear Freesurfers,
>
> after running the average subject with Freesurfer 5.3, the files T1.mgz and
> Orig.mgz were not created in the fsaverage folder. Where could be the problem?
Some steps are volume-based and some are surface-based. Motion
correction is voxel based. Slice-timing correction is done in the
volume. It then gets sampled onto the surface where surface-based
smoothing is done. The GLM analysis is done on the surface. I often use
voxel and vertex interchang
Thanks David!
Gabriella
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of David Vazquez
Sent: Friday, May 22, 2015 6:19 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] FW: correcting for brain size
Hi Gabriella,
I'm not an exp
no ./rh.unknown.label was created.
Yawu
On Mon, May 25, 2015 at 7:22 PM, Douglas Greve
wrote:
> Is there a file called ./rh.unknown.label ?
>
>
>
> On 5/25/15 5:37 AM, Liu Y wrote:
>
> Dear Freesurfers,
> I tried to generate annotations by using the command mris_label2annot --s
> K_TS66 --
Hi Hassan
that's not the correct command line for tkmedit. You are probably better
off using freeview in any case though, once you make the binary
executable.
cheers
Bruce
On Tue, 26 May 2015, Hassan bakhshi wrote:
Hello,
I had the problem which was the recon-all error at "Fix Topology lh"
Hi Hassan
try:
chmod a+x FREESURFER_HOME/bin/freeview.bin
cheers
Bruce
On Tue, 26 May 2015, Hassan
bakhshi wrote:
Hi I downloaded the centos 6 freeview.bin and replaced it into
$freesurferhome/bin/freeview.bin
but now i cant open freeview, it says that it is not a executable file and
it i
Hi Hassan
the cortical stats are generated by mris_anatomical_stats while the
noncortical ones (like hippocampal volume) by mri_segstats. The results
of each are tabulated in each subject's stats dir.
cheers
Bruce
On Tue, 26 May 2015,
Hassan bakhshi wrote:
> Hi,
> I wanted to ask what is the
Hi Sofia
can you email us the command line you ran to create the average subject
and its output?
thanks
Bruce
On Tue, 26 May 2015, Sofia Rodriguez Penuela wrote:
Dear Freesurfers,
after running the average subject with Freesurfer 5.3, the files T1.mgz and
Orig.mgz were not created in
Did you check the permissions? You have to make sure the permissions are
executable.
HTH
D
On 5/26/15 6:33 AM, Hassan bakhshi wrote:
> Hi
> I downloaded the centos 6 freeview.bin and replaced it into
> $freesurferhome/bin/freeview.bin
>
> but now i cant open freeview, it says that it is not a ex
Hi,
I wanted to ask what is the difference between stat files result and the
mris_anatomical_stats?
can we get the same result using both?
i want to get the anatomical thickness of temporal gyruses such as superior
temporal gyrus thickness, and non neocortex volumes like hippocamp and
amygdala v
Hi
I downloaded the centos 6 freeview.bin and replaced it into
$freesurferhome/bin/freeview.bin
but now i cant open freeview, it says that it is not a executable file and
it is binary.
i wanted to test hippocampal subfields.
Kind regards
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Freesurfer
Hi again,
The software requires approximately 10GB of RAM
Cheers
Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: Erik O'Hanlon
To: Freesurfer supp
Hello,
I had the problem which was the recon-all error at "Fix Topology lh" stage
for 6 of 12 subjects i ran freesurfer.
Bruce then told me to check the lh.orig.nofix and lh.inflated.nofix to see
if there is part of skull or cerebellum.
But when i want to open them with this command:
tkmedit lh.o
Hi Eugenio,
I'm trying to run in on a cluster and I think I have eight cores assigned with 2GB per core. I'm not sure if the process is parallelised though so it could be the case that I have the job running on one of the possible core and only using 2GB of RAM. I can
ask the cluster support
Hi Angela,
It will work with subjects processed with the previous version; however, I
would recommend (if possible) to run everything with the same version, for the
sake of reproducibility.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal
Hi Erik,
I guess your process was killed by the kernel. Maybe you ran out of RAM memory?
How much RAM do you have?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Or
Dear Freesurfers,
after running the average subject with Freesurfer 5.3, the files T1.mgz
and Orig.mgz were not created in the fsaverage folder. Where could be
the problem?
Thank you in advance.
Best regards,
Sofia
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