Hi FreeSurfer experts!
We have isotropic T1/T2 and FLAIR volumes for a larger cohort. It would be
fine to use the T2 / FLAIR volumes to improve the segmentation and to
perform a couple additional analyses using FS. This leads to the following
questions:
1) How do I incorporate T2/Flair
Hi Analstasia,
as you suggest, adjusting brain mask the tracts are better. Now I'd like to
perform trac-all with new version by using a new configuration file.
I do not understand what I should do for:
1- set b0mlist2- set b0plist
Thanks.
Stefano
Messaggio originale
Da:
Hi list,I'm performing qdec. This my file.dat1 diagnosis discrete 21
Pathology2 Controls2 Thickness_lh continuous 03 Thickness_rh
continuous 04 NPStest continuous 0Continuous Factors:
Mean: StdDev:--- -
On 03/25/2013 02:09 PM, Douglas N Greve wrote:
Dear FreeSurferers, it has just come to my attention that there may be a
bug in the way that QDEC computes contrasts for DOSS. If you are using
QDEC in this way, please hold off until I track down the problem. Also,
please let me know if you
1a) You would do this after running recon-all on the T1-weighted image. It
will only adjust the surfaces, not the segmentation. Something like
recon-all -T2pial path to flair
1b) this will work with either, but in my experience the FLAIR helps more
to distinguish dura from gm
2) Yes. The
eek, that's pretty bad. No idea why that would happen. Can you send us
the recon-all.log? If you rerun with the original brain.finalsurfs.mgz
does it restore good surfaces?
On Thu, 28 Mar 2013,
preci...@nmr.mgh.harvard.edu wrote:
Hello Freesurfers,
I ran recon-all on a subject's structural
well, something is really wrong. Did you happen to change the voxel type of
brain.finalsurfs.mgz? Can you run mri_info on it and send us the results?
If not, then upload the tarred and gzipped subject dir and I'll take a
look. I don't think it will be hard to fix
On Thu, 28 Mar 2013,
mri_info for both attached.
Interestingly enough, brain.finalsurfs.manedit.mgz is significantly larger
in size. If it was a copy of the other, shouldn't it be the same size?
Also, brain.finalsurfs.manedit.mgz shows a time/date stamp from the last
time I edited it and brain.finalsurfs.mgz has a
Hi, freesurferers
I am trying to execute the post installation tests as recommended at
Freesurfer Wiki.
Using a CentOS6 Virtual Machine (kernel 2.6.32-358.2.1.el6.x86_64) over
Fedora 18 using VirtualBox 4.2.8. Freesurfer version is 5.2. Tkmedit,
Tksurfer, qdec and freeview all work great.
All versions are affected.
doug
On 03/28/2013 08:34 AM, jm wrote:
On 03/25/2013 02:09 PM, Douglas N Greve wrote:
Dear FreeSurferers, it has just come to my attention that there may be a
bug in the way that QDEC computes contrasts for DOSS. If you are using
QDEC in this way, please hold off
I find the T2w image works well for removing dura and blood vessels, but
I'm not sure FLAIR would work for T1w/T2w myelin mapping because of what
would happen to the ratio near the pial surface.
Instructions for T1w/T2w myelin mapping are available here:
Dear Matt!
Thanks a lot. We do have both FLAIR and T2 - so I could use the FLAIR for
the clean-up procedure and use the T2 volumes for myelin part...
Best wishes,
Luke
Matt Glasser
Hi Stefano - Nothing has changed with these variables between 5.1 and 5.2.
So do with them whatever you were doing before.
a.y
On Thu, 28 Mar 2013, std...@virgilio.it wrote:
Hi Analstasia,
as you suggest, adjusting brain mask the tracts are better.
Now I'd like to perform trac-all with
Hi Jon - The command that fails is trying to multiply 2 volumes and
complains that they have different sizes. Have you checked if these 2
volumes exist and what their dimensions are?
a.y
On Wed, 27 Mar 2013, Jon Wieser wrote:
i ran
trac-all -prep -c dmrirc_single_subject
and got the error
Hello list,
I have a group of subjects (4 patients and 8 controls) in which one
MPRAGE sequence was used and another group of subjects (2 patients and
2 controls) where a diffent MPRAGE was used. Both groups were acquired
in the same scanner. For each subject I have two anatomical
Hi Nawaf - Can you please send your trac-all.log? It's possible that the
problem started at an earlier step.
Thanks,
a.y
On Thu, 28 Mar 2013, Nawaf Yassi wrote:
Dear mailing list
I am encountering an error at the trac-all –path stage of a tracula analysis
(the
first two stages on
Hi Sal,
1. I have no experience with the sun grid engine, perhaps someone else on
the list can help with that.
2. The -bedp step needs the outputs from the -corr and -masks steps. The
-path step needs the outputs from the -bedp step. The output files from
each part are listed here:
You can open them in a viewer, or just run mri_info on them.
On Thu, 28 Mar 2013, Jon Wieser wrote:
How do i check the dimensions of the volumes?
Jon
- Original Message -
From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer
Hi Ping - It'll make it easier for us to replicate your memory error if
you send us the data set where you get the error. Can you please zip up
the dmri, dmri.bedpostX, and dlabel directories for this subject and
upload them for me and Zeke?
https://gate.nmr.mgh.harvard.edu/filedrop2/
Dear Freesurfer experts,
I'm trying to investigate lh-to-rh asymmetry, so I register my subjects to
the subject of fsaverage_sym following the instructions on this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. After all the surfreg
commands I've got ?h.thickness files in
it really depends on what the differences are. The best thing to do would
be to scan some controls with both sequences and see what the differences
are, although that won't rule out some disease-specific differences that
you only see in the patients
On Thu, 28 Mar 2013, _andre...@sapo.pt
p.s. you would be better off if you had the same proportion of patients
and controls with each sequence. Matching the numbers within one sequence
and not the other doesn't really help
On Thu, 28 Mar 2013, _andre...@sapo.pt
wrote:
Hello list,
I have a group of subjects (4 patients and 8
Hi Bruce,
I did that test some time ago (each sequence alone or averaged) but
only with one control subject. I then checked the values of different
measures and the cortical thickness maps for each situation and they
were very similar indeed. I did it only with one subject because the
It says no such file or directory
does rh.perifhyinal.label exist?
On 03/28/2013 11:55 AM, std...@virgilio.it wrote:
Hi list,
I'm running perirhinal analysis with this error:
mri_label2label --srcsubject fsaverage --srclabel rh.perirhinal.label
--trgsubject Con01 --trglabel
On 03/28/2013 12:16 PM, Ejoe Yizhou Ma wrote:
Dear Freesurfer experts,
I'm trying to investigate lh-to-rh asymmetry, so I register my
subjects to the subject of fsaverage_sym following the instructions on
this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. After all
the surfreg
Actually, #2 will not work. I don't think you can use qdec with the
xhemi stuff anyway. You should use the mris_preproc command followed by
mri_glmfit.
doug
On 03/28/2013 12:51 PM, Douglas N Greve wrote:
On 03/28/2013 12:16 PM, Ejoe Yizhou Ma wrote:
Dear Freesurfer experts,
I'm trying to
Hi folks,
sorry it's me again with a very basic question. What is the best way to
import longitudinal data?
recon-all -i /path/T1A.nii -i /path/T1B.nii FIRSTSUBJECT
or
recon-all -i /path/T1A.nii FIRSTSUBJECT_A
recon-all -i /path/T1A.nii FIRSTSUBJECT_B
I tend to use the second choice because
Thanks, Doug.
I'm not planning to use qdec. It's just that I used to generate the
?h.thickness_max10.fwhm10.fsaverage_510.mgh files (which are what we name
the files after running the two commands) before I use mris_preproc and
mri_glmfit. I also generally skip the smooth step in freesurfer
Hi Luke
if I understand you properly the second way it the correct way (assuming
T1A.nii and T1b.nii are two timepoints for a subject). I think you have a
typo though as your second recon-all should use T1B.nii as input.
cheers
Bruce
On
Thu, 28 Mar 2013, lukas.sch...@ukb.uni-bonn.de
Hi Cherry, what I meant was that you cannot use the qcache with xhemi.
You'll need to run the mris_preproc command as listed on the web page.
doug
On 03/28/2013 01:00 PM, Ejoe Yizhou Ma wrote:
Thanks, Doug.
I'm not planning to use qdec. It's just that I used to generate the
Yes, it is located in
/Applications/freesurfer/subjects/subject_prova/Con01/label/rh.perirhinal.label.
Stefano
Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 28-mar-2013 17.46
A: freesurfer@nmr.mgh.harvard.edu
Ogg: Re: [Freesurfer] perirhinal analysis
It says no such file
I see. Then I think I'd better just follow the instructions on the Xhemi
page. Thanks!
On Thu, Mar 28, 2013 at 1:06 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Hi Cherry, what I meant was that you cannot use the qcache with xhemi.
You'll need to run the mris_preproc command as listed
If the source subject is subject_prova then you need to spec that subjet
2with --srcsubject (instead of fsaverage)
doug
On 03/28/2013 01:11 PM, std...@virgilio.it wrote:
Yes, it is located in
/Applications/freesurfer/subjects/subject_prova/Con01/label/rh.perirhinal.label.
Stefano
Hi Freesurfers,
I'm in the middle of coregistering a CT and MRI, and after running
spmregister --s MGXX_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol orig
I get the error that orig.mgz is not found in COR or MGZ formats, but I have an
orig.mgz file in my folder. Any help on this would be
Hi All,
Am I right in reading the dev table that if I just want the aseg.mgz, (not
the stats output), I only need to run auto-recon1 and auto-recon2?
I need to run 250+ brains just to get the aseg volume, so if I can shave
off 4-10 hours off each that would be huge.
Make sure that there is an orig.mgz in $SUBJECTS_DIR/MGXX_SurferOutput/mri
Also, make sure to send the full terminal output
doug
On 03/28/2013 02:13 PM, Borzello, Mia wrote:
Hi Freesurfers,
I'm in the middle of coregistering a CT and MRI, and after running
spmregister --s MGXX_SurferOutput
In fact, couldn't I stop after calabel if all I want is the aseg.mgz?
-
Josh
On Thu, Mar 28, 2013 at 11:18 AM, Joshua Lee jki...@ucdavis.edu wrote:
Hi All,
Am I right in reading the dev table that if I just want the aseg.mgz, (not
the stats output), I only need to run auto-recon1 and
Hi Josh,
yes, I think that's correct.
Bruce
On Thu, 28 Mar 2013, Joshua Lee wrote:
In fact, couldn't I stop after calabel if all I want is the aseg.mgz?
-
Josh
On Thu, Mar 28, 2013 at 11:18 AM, Joshua Lee jki...@ucdavis.edu wrote:
Hi All,
Am I right in reading the dev
Hi Freesurfer group, Im attempting to use FS-FAST with resting BOLD data,
and I have come across the following error.
I tried changing files to non .gz extension, and still have this error..
$Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $
`fast_selxavg3' is a script from the file
Still stuck with this error in my QDEC analysis attempt, at my wit's end,
could anyone help please? Thanks!
Tudor
On 26 March 2013 20:35, Tudor Popescu tud...@gmail.com wrote:
Just giving this thread a new bump, as *again *I am receiving this error
from mri_concat, upon pressing the Analyze
I was wondering if anybody is able to help with (any one of) these
questions? That would be really helpful, as I could not find an answer on
the wiki.
Many thanks in advance!
On 26 March 2013 20:44, Tudor Popescu tud...@gmail.com wrote:
Hi everyone,
My QDEC analysis ran into an error
Hi, Josh, I think you can run the autorecon1, subcortseg and no segstats if
you don't want the statistics file (aseg.stats). Also, use -openmp 8 can
speed up quite a lot by multi-threading. For a regular T1 brain image, I
can the running time to get aseg.mgz in about 4-5 hours.
recon-all -i
make sure to add the following lines to your ~/matlab/startup.m
FSH = getenv('FREESURFER_HOME');
fshmatlab = sprintf('%s/matlab',FSH);
path(path,fshmatlab);
clear fshmatlab FSH;
doug
On 03/28/2013 03:48 PM, Mario Ortega wrote:
Hi Freesurfer group, Im attempting to use FS-FAST with resting
Sorry, I've totally lost track of this thread. Are you able to run
mri_concat outside of QDEC?
On 03/28/2013 03:51 PM, Tudor Popescu wrote:
Still stuck with this error in my QDEC analysis attempt, at my wit's
end, could anyone help please? Thanks!
Tudor
On 26 March 2013 20:35, Tudor
On 03/28/2013 03:53 PM, Tudor Popescu wrote:
I was wondering if anybody is able to help with (any one of) these
questions? That would be really helpful, as I could not find an answer
on the wiki.
Many thanks in advance!
On 26 March 2013 20:44, Tudor Popescu tud...@gmail.com
nope, you wouldn't benefit any further I don't think
On Thu, 28 Mar 2013,
Joshua Lee wrote:
Hey thanks,
I haven't worried about multi threading typically since I just run more
brains simultaneously. On my computer, I have sufficient 64 gigs RAM (64
gigs) and 24 CPU/cores (not sure which) to
Jorge,
Thanks for the clarification. I will try an analysis using [1 2 3] with all of
the subjects with a minimum of 4 repeats and compare the results using the same
analysis on all subjects with a minimum of 3 repeats. This is worthwhile for
us since we lose quite a few when excluding those
Hi Francois
I think that you missunderstood a point of my previous answer. You should
always include ALL subjects (those with 1,2,3,4... and so on repeated measures)
in your analysis whether or not the model for the covariance includes one, two,
three or more random effects.
What I wanted
Here are the errors from the trac-all.log file I sent earlier:
mri_convert ERROR: could not determine file for
/mnt/glusterfs/salsoman/output/FS/Test_FS/mri/ERROR:
/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister.nii
mri_convert ERROR:
It was brought to my attention that the previous link was broken. Here is a
corrected link:
http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2656.2002.00618.x/abstract
The paper reference is:
On the misuse of residuals in ecology: regression of residuals vs. multiple
regression
1. Robert P.
Hi freesurfers,
I working on a coregistration right now with a few different CT scans. None of
them have looked that good with tkregister (for example when I used one CT
scan, the electrodes didn't even show up). Is there an certain CT I need to be
using?
Thanks,
m
Contrast creation is the same in all programs. It is based on the design
matrix.
Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
On Wed, Mar 27, 2013 at 2:53 AM, xiangbo_2010 xiangbo_2...@126.com wrote:
Dear Prof Donald McLaren
I am sorry to disturb you! I have four discrete variables {factor 1(A,B),
factor 2(C,D), factor 3(G,H), and gender(M,F)} and a continuous variable
(age), I want to use the GLM to analysis the
Hi freesurfers,
In using tkregister, I generated an odd (see attached): the image not only
looks sheered but there is an old white box showing up. I'm not sure how to
resolve this.
Thanks a lot,
Mia
attachment: freesurfer.PNG___
Freesurfer mailing
Hi FS experts:
I am trying to map AAL template onto FS surface to create surface-based AAL
template. Several days ago, i asked this question, and Garikoitz Lerma gave me
some suggestions. Possibly, i think the process is like as folllows:
1. downloa the Colin27 subject in Surfrend page,
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