Hello Doug,
Each individuals subject data has already been smoothed by 5 10 15 20 and
25 through the qache function during the initial processing.
I'm a little confused now. I thought that the mri_preproc would use the
non-smoothed values of the subjects and create an mgh file. After which I
smoo
Hi Chris,
still the same (kind of) problem. For some reason you are getting an
empty line in the qdec table so it expands the name to
".long." . Open your long.qdec.table.dat in an editor (e.g. nedit or
gedit), maybe try to copy it into a new editor window, safe it and hope
the editor fixes t
Oh, I see it would prevent us from getting the aseg.stats file.
That's not good; we want the whole enchilada :-)
Never mind; will follow your previous suggestion and run recon-all all the
way through;
Thanks Doug;
Mehul
On Tue, Jun 4, 2013 at 11:41 AM, Douglas N Greve
wrote:
>
> It would sto
Hi Doug,
Thanks; Will do so.
Also I forgot to mention one thing in the previous email:
for case -autorecon3, also there is:
set DoSegStats = 1; (in recon-all script in 5.3 this is line 5526)
would it help, if "set DoSegStats = 1" was used only in -autorecon3
and not in the
-autorecon2
Hi Doug,
Yes, we see the same error as in msg28047.html; here is the line from my
recon-all.log:
mghRead(/mnt/horizon/stage/HLC//004_151_3106223/WBS/Baseline/Freesurfer/mri/ribbon.mgz,
-1): could not open file
In msg28047.html, Milkos suggested that the issue could be the following
line in re
I saw this issue too.
The total running time went from an average of 16.3h to 20.4h
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist
ok, thanks
On Tue, 4 Jun 2013, Mehul Sampat wrote:
Hi Bruce,
Okay. It went from ~4 hours in 5.2 to ~9 hours in 5.3; we thought it was a big
change to
and are trying to isolate the root cause
We are running 75 cases run with 5.3 that have been run with 5.2 before;
once they are done, will l
Hi Bruce,
Okay. It went from ~4 hours in 5.2 to ~9 hours in 5.3; we thought it was a
big change to
and are trying to isolate the root cause
We are running 75 cases run with 5.3 that have been run with 5.2 before;
once they are done, will let you all know if this issue is seen in other
cases too.
>
> Hi Doug,
>
> The command runs a bit further now but then exits with errors.
> Unfortunately this time there is no specific stated error. The last few
> lines of the log are:
>
> INFO: extension is mgz
> #
> #@# Talairach Tue Jun 4 13:22:08 EDT 2013
>
Make sure that your SPM volume is registered to the anatomical, then use
mri_vol2surf to map the volume to the surface, then mri_segstats to
extract the mean of the thickness
doug
On 06/04/2013 01:45 PM, Ozranov-Palchik, Ola wrote:
>
> main lab: (617) 355-0400
Dear FreeSurfer Experts,
I w
Dear FreeSurfer Experts,
I was wondering if anyone can advise on the best way to use an ROI mask created
in SPM (XjView) to extract cortical thickness values in freesurfer.
Thank you in advance for your help!
Ola
Ola Ozranov-Palchik M.S.
Research Coordinator, Gaab Lab
Laboratories of Cognitive
Dr. Reuter,
Thanks for your help, it got me through the error I was having. On to the
next one:
When I enter the command:
mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target fsaverage
--hemi lh --meas thickness --out lh.thickness.mgh
it spits out the following two lines before quittin
Hi Mehul
no, that's definitely not expected for it to go from 20 min to almost 5
hours! We'll investigate as that shouldn't be the case.
Bruce
On Tue, 4 Jun 2013, Mehul Sampat wrote:
In some cases, we are seeing that, for the same subject, the run time is slower
for 5.3 versus 5.2;
A qui
Dear FreeSurfers!
I want to do bias correction on some T1 and T2 images. I have heard that
you can do this by using mri_nu_correct.mni
how should I use this command?
I could not understand this (I am a beginner in FS) :
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_nu_correct.mni
would it be s
Sorry for the bunch of emails. I registered and got the license file. I have
been using this software after a long time and feel silly that this was the
thing that was causing trouble. Thank you Doug!
Manish
From: Douglas N Greve
To: freesurfer@nmr.mgh.harvard
Hi Rafa
this doesn't look like the whole subject dir, just some files from it
(e.g. no mri/transforms/talairach.xfm). Don't email it to me - use our
ftp site
cheers
Bruce
On Tue, 4 Jun 2013, Rafa X wrote:
Hi Bruce,Thanks for your reply. I have attached the zipped subject dir (please,
note
Ok I checked the other version of freesurfer and I do have .license file in the
freesurfer folder. How can I get this file?
Best,
Manish
From: Douglas N Greve
To: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, June 4, 2013 10:15 AM
Subject: Re: [Freesurfer] F
yes, there is a file called LICENSE in the freesurfer folder. Should I look for
something else?
Thanks,
Manish
From: Douglas N Greve
To: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, June 4, 2013 10:15 AM
Subject: Re: [Freesurfer] Freesurfer error..recon-all f
Does the license fileexist? Note it is not called license.txt
On 06/04/2013 12:13 PM, Manish Dalwani wrote:
> Hello Freesurfer's
>
> I am working on the MAC OS 10.8 and just recently installed the
> freesurfer on this server machine.
>
> I have checked the permissions to various and folders and th
Hi Octavian
not sure what eT2W FLAIR sense is. The T2_SPACE flair is the only one
that we have routinely used that has about 1mm isotropic resolution, and
yes we will take care of the registration. Whatever FLAIR you use just
point FreeSurfer at it (nifti or dicom)
cheers
Bruce
On Tue, 4
Hello Freesurfer's
I am working on the MAC OS 10.8 and just recently installed the freesurfer on
this server machine.
I have checked the permissions to various and folders and they look ok to me.
When I run the following command:
recon-all -i MR100021.dcm -s test2
I get the following err
isn't that a feature? Freeview saves state to try to preserve the
appropriate settings.
As for recon-all, yes that is the way it works. If you want to start with a
new volume with -i you have to delete the subject dir (or specify a newly
named one)
cheers
Bruce
On Tue, 4 Jun
2013,
obre...@
Dear All,
Among T2 FLAIR, eT2W FLAIR sense, T2, which sequence should be preferably
used as auxiliary for pial definition?
Does Freesurfer take care of coregistration between these and the MPRAGE?
What would be the command line (Linux Ubuntu) if I want to use SPM
generated nifti DICOM concatenatio
That dcmunpack command will put the data into a file called
unpack3/MPRAGE/002/struct.nii
It needs to be put into upack3/mri/orig/002.mgz
doug
On 06/04/2013 11:22 AM, Nitenson, Adam wrote:
> Hi Doug,
>
> When I try the command as you suggested:
> recon-all -all -s unpack3
> I get the following
Hi Bruce,
This is certainly something I want to avoid, I guess I won't be using the
-motioncor flag in any of my studies!
I ran recon-all using both only one and two (motion corrected and
averaged) source volumes, and the results do seem to suggest that using
one vs. two volumes is an empirical i
--no-sim takes an argument. Run mri_glmfit-sim with --help to get more info
doug
On 06/04/2013 09:11 AM, Glen Lee wrote:
> Hi Doug,
> I tried as you suggested, but i've got the following error:
> e.g.,cannot find any csd files.
> However, I can see them stored in csd folder as shown below:
>
>
Hi Doug,
When I try the command as you suggested:
recon-all -all -s unpack3
I get the following error:
ERROR: no run data found in
/gpfs/data/twhite/anitenso/FreesurferPractice/unpack3/mri. Make sure to
have a volume called 001.mgz in
/gpfs/data/twhite/anitenso/FreesurferPractice/unpack3/mri/ori
Thanks!!
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Tuesday, June 04, 2013 9:51 AM
To: Ray, Siddharth
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_convert mgz to nifti
mri_convert file.mgz file.nii.gz
should do the trick
On Tue, 4
The command is 'mri_convert' not 'Mri_convert' -- at least on case
sensitive filesystems (like Linux and some-but-not-all Mac OS X).
On 6/4/13 10:46 , Ray, Siddharth wrote:
>
> Hi all,
>
> I just want to convert .mgz files to .nifti using mri_convert, do I
> have to flip my image when I do that
mri_convert file.mgz file.nii.gz
should do the trick
On Tue, 4 Jun 2013, Ray, Siddharth wrote:
Hi all,
I just want to convert .mgz files to .nifti using mri_convert, do I have to
flip my image when I do that using RAS ? or I should
simply use:
Mri_convert input_file_name.mgz output_
Hi all,
I just want to convert .mgz files to .nifti using mri_convert, do I have to
flip my image when I do that using RAS ? or I should simply use:
Mri_convert input_file_name.mgz output_file_name.nii
Thanks in advance,
Siddharth
___
Freesurfer ma
Hi all,
I would like to save copy of the CentOS5 release of Freesurfer in my group's
work space as described in the email below. The link in the email that is
supposed to explain this doesn't work; could someone please let me know how to
do this or point me to another webpage that explains it?
I would probably leave out the fissure, but not the fimbria...
Cheers,
/Eugenio
On Tue, 2013-06-04 at 14:33 +0200, Claudia Dacquino wrote:
> Hi guys!
> I have a dataset including hippocampal subfields obtained through the
> -hippo-subfields flag. I want to have a measure of total hippo volume
> an
hi bruce,
thanks. from the reading of "recon-all" it looks like this is a failure is
occurring in the latter part of autorecon3 so I'm just rerunning that set
and skipping autorecon2 on the subjects that failed.
correct?
best,
-robert
On 6/4/13 9:38 AM, "Bruce Fischl" wrote:
p.s. you can ch
p.s. you can check to see if those labels exist in your fsaverage/label
dir
On Tue, 4 Jun 2013, Welsh, Robert wrote:
> ah, that probably got there from the 5.2 recon-all. I'll go in and
> manually change those.
>
> thanks
>
> -robert
>
>
> On 6/4/13 8:59 AM, "Bruce Fischl" wrote:
>
> Hi Robert
>
ok, let us know if it fixes your problem
Bruce
On Tue, 4 Jun 2013, Welsh, Robert
wrote:
> ah, that probably got there from the 5.2 recon-all. I'll go in and
> manually change those.
>
> thanks
>
> -robert
>
>
> On 6/4/13 8:59 AM, "Bruce Fischl" wrote:
>
> Hi Robert
>
> I think you need to symlin
ah, that probably got there from the 5.2 recon-all. I'll go in and
manually change those.
thanks
-robert
On 6/4/13 8:59 AM, "Bruce Fischl" wrote:
Hi Robert
I think you need to symlink the fsaverage dir to the 5.3 fsaverage
instead of 5.2
cheers
Bruce
On Tue, 4 Jun 2013, Welsh, Robert wrote:
Hi all,
In our efforts to take our 5.2 edits to 5.3 we tried the command below (in the
attached thread), but we also tried the command
recon-all –s [subject-d] -autorecon2 –autorecon3
and those jobs are also running for some time but then crashing with the same
error complaining that lh.BA1.th
Hi Doug,
I tried as you suggested, but i've got the following error: e.g.,cannot
find any csd files.
However, I can see them stored in csd folder as shown below:
/2D/results/LH/GLM/csd> ls
mc-z.negative.j001-osgm.csd perm.abs.2.j001-osgm.csd
I'm guessing that I need to define the path for this
Hi Oscar
what do you mean by "the CSF surface"? Outside the brain or in the
ventricles? If outside, there is some code for creating boundary element
models for EEG/MEG analysis.
There is no trivial way to create a single surface. The way I've done it in
the past is to replace the lh or rh va
Hi Rafa
that sounds like a bug. Can you gzip and upload the whole subject dir?
cheers
Bruce
On
Tue, 4 Jun 2013, Rafa X wrote:
Dear freesurfer experts,
I was running an autorecon2 in the recon-all but always gives me this memory
allocation error, only on this
subject. Im using FS v5.1
#@
Dear Dr Greve,
Together with Dr Hilde Huizenga I am implementing an fMRI study in which we
would like to optimize the design by using Optseq2. We have a few
questions. Could you please help us out?
Our task consists of 3 runs of 72 trails each, in which participants are
presented with a fixation
Hi Robert
I think you need to symlink the fsaverage dir to the 5.3 fsaverage
instead of 5.2
cheers
Bruce
On Tue, 4 Jun 2013, Welsh, Robert wrote:
Hi,
We were re-processing a subject to test the fix for 5.2 to 5.3. The initial
recon-all and subsequent autrecon2
and autorecon3 were run a few
Hi guys!
I have a dataset including hippocampal subfields obtained through the
-hippo-subfields flag. I want to have a measure of total hippo volume and
I'm not sure which structures should I include in the sum. I was thinking
to exclude fimbria and fissure and sum the others. Am I right? Or shoul
Dear all,
I need to extract three surfaces from MRI data:
- GM-WM interface -> thus, lh.white and rh.white would be the answer.
- Pial interface -> thus, lh.pial + rh.pial
- CSF surface
For CSF, as far as I know, the best option would be to generate a binary
volume merging the appropriate labels
Hello All,
I have run recon-all on some subjects. I have functional BOLD data on these
subjects too. I am doing fmri preprocessing in spm. I have created register.dat
by registering the meanBOLD image to the freesurfer reconstructed data. I am
intending to do the following -
I want to take eac
Hello FreeSurfers,
after reading this [1] paper about measuring surface area, i realized i don't
know what the default way of measuring surface area is in FreeSurfer. Is it
similar to what's described in the paper? Could you point me to the right
documentation or publication?
Forgive me if i've
A three-year term position as Postdoctoral Fellow (governmental
position code 1352) is available at the Norwegian Centre for Mental
Disorders Research (NORMENT) and the KG Jebsen Centre for Psychosis
Research – TOP Study Group, Institute of Clinical Medicine, University
of Oslo and Oslo Univers
Dear freesurfer experts,
I was running an autorecon2 in the recon-all but always gives me this
memory allocation error, only on this subject. Im using FS v5.1
#@# ASeg Stats Mon Jun 3 20:13:11 CEST 2013
/root/trabajo/freesurfer/subjects/qsm1_17_stats2_g
mri_segstats --seg mri/aseg.mgz --sum
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