Dear FS users,
can anybody help me in understanding the results of the localGI pipeline?
After calling the
recon-all -s *subj *-localGI
recon-all -s *subj* -qcache -measure pial_lgi
mri_segstats --annot *subj *lh aparc --i $SUBJECTS_DIR/*subj*/surf/lh.pial_lgi
--sum lh.aparc.pial_lgi.stats
wh
Hi all,
I am now working with the 5.3 version and performing interhemispheric
registration (building my own atlas)
after running for all subjects:
xhemireg --s subj001
surfreg --s subj001 --t fsaverage_sym --lh
surfreg --s subj001 --t fsaverage_sym --xhemi --lh
I have tried first iteration, b
Dear Doug,
Thanks for the quick response. I will try running the analyses on the command
line. I've put the whole error message here if that is of any use and sheds any
light to the problem? https://www.dropbox.com/s/1h1wzwidt3k1scu/ErrorMessage.txt
Also, when I try to plot the stats tables us
Hi Marie,I've attached the log file.Thanks very much,Sarina Iwabuchi
This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do no
I have an MPRAGE dicom file sequences on which I wish to run recon-all .
Here is the command I am using:
mri_convert DICOM_DIRECTORY SubjectName/mri/orig/001.mgz
It returns immediately with the error message:
corRead(): can't open file DICOM_DIRECTORY/COR-.info
Your suggestions would be welc
Hi Don
you don't need to convert the dicom series, just point recon-all at ONE
file in the mprage series:
recon-all -i \
-s -sd -all
the list of labels is in $FREESURFER_HOME/FreeSurferColorLUT.txt,
although it contains some labels for structures that we don't routinely
segment (yet!).
Hi Freesurfer team,
I am running into an issue when I am specify the -hemi flag for the recon
-all command (in this case recon -all -hemi rh). The command seems to work
for the most part, except it errored at the end and seemed to be looking
for a file for the other hemisphere. How do I get this c
HI freesurfer experts,
I am running a qdec analysis, my first factor has 3 levels, my other 2 factors
have 2 levels, I select my first and second factors and hit "Analyze"
I get the error ? :
Error in Analyze: command failed
ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 level
Hi,
I had successfully reconstructed a primate brain using fs5.3. But one part of
left anterior temporal lobe was not correct, even with the accurate wm.mgz.
See attached image for what I mean. Are there parameters to be used to correct
this problem?
Thanks,Xiaomin
Hi Elisa,
It is recommended to use lGI on a vertex-wise basis, i.e. to use qdec the same
way you would for cortical thickness. To get access to pial_lgi as a measure of
interest in qdec, you need to add a row with: MEASURE1 = pial_lgi in the
.Qdecrc file located in your home directory.
Otherw
On 29 Jul 2014, at 11:29, Sarina Iwabuchi wrote:
>
> Hi Marie,
>
> I've attached the log file.
>
> Thanks very much,
>
> Sarina Iwabuchi
>
>
> This message and any attachment are intended solely for the addressee and may
> contain confidential information. If you have received this message
Dear Fs Experts,
What is the difference between (wm.mgz and wm.seg.mgz)_ in the output of
recon-all? i.e is wm.mgz means the whole white matter (right_left hemispheres
and brain stem except the cerebellum)
Thanks
Mohamad
___
Freesurfer mailing list
Fre
Hi Talia
we need more information to help you. Have you looked at the wm.mgz? Is it
accurate? What about the ?h.orig and ?h.orig.nofix surfaces?
You need to track down where in the pipeline things started going wrong.
cheers
Bruce
On Mon, 28 Jul 2014, Talia Raney
wrote:
> Hi,I'm having issu
Hi Sarina,
Thanks for the log, I see better the problem. However I unfortunately don't
know the answer. The lGI calls MRIread and load_mgh, and the error seems to
related to load_mgh.m itself.
Bruce / Doug / Nick, any guess what can yield such a "switch expression must be
a scalar or string c
Hmmm, I'm not sure what is going on either. The problem seems to be that
the file is not getting unzipped (and so does not have anything to do
with the switch statement per se).
Sarina, try going into matlab and running
a =
MRIread('/Volumes/HD-PNTU3/MISSEDDATA/extn003/surf/tmp-mris_compute_l
Hi Mohamad
the wm.seg.mgz is the output of mri_segment and is a voxel segmentation
that considers local intensities and estimated cortical geometry, but not
topology. mri_pretess then takes the wm.seg.mgz and removes certain
pathological voxel configurations (like corners touching) that mess u
Dear Freesurfers
I want to apply the transform matrix talairach.xfm, to a set of discrete
points.
(in order to get mni coordinate and use template brain).
These are electrodes, with coordinates in the brain.mgz space.
Here is what I did following the advices from the Coordinates systems page :
get
the white is a region on the midline, probably ventricle, that we fill to
create a closed surface for the cortical models. If you want a white
matter mask you are better off extracting it from the aseg.mgz with
mri_binarize -match
cheers
Bruce
On Tue, 29
Jul 2014, Alshikho, Mohamad J. wrote:
I'm getting the following erorr when running Qdec "Analyze"
Model Factors:
Discrete (fixed factors)
ADHD_Persist
MJ_group
Nuisance factor:
Age
ERROR: matrix is ill-conditioned or badly scaled, condno = 10355.4
Possible problem with experimental design:
What is the command line that is failing and what is the full terminal
output?
doug
On 07/29/2014 05:55 AM, angela.fav...@unipd.it wrote:
> Hi all,
> I am now working with the 5.3 version and performing interhemispheric
> registration (building my own atlas)
>
> after running for all subjects:
On 07/29/2014 06:26 AM, Isotalus, Hanna wrote:
> Dear Doug,
>
> Thanks for the quick response. I will try running the analyses on the command
> line. I've put the whole error message here if that is of any use and sheds
> any light to the problem?
> https://www.dropbox.com/s/1h1wzwidt3k1scu/Err
You have to tell it not to do all the operations after the per-hemi
phase. At one point, it used to be easy to do this, but I don't think
anyone ever used the per-hemi operations and now it might not be possible.
doug
On 07/29/2014 10:40 AM, C. Paula de los Angeles wrote:
> Hi Freesurfer team,
you can't in QDEC. You'll have to use the command line stream
doug
On 07/29/2014 10:43 AM, Jon Alan Wieser wrote:
>
> HI freesurfer experts,
>
> I am running a qdec analysis, my first factor has 3 levels, my other 2
> factors have 2 levels, I select my first and second factors and hit
> "Analy
that sounds like a problem with the registration/transformation not the
mask itself. Why are you doing only translation? There will certainly be a
rotation. Have you tried using bbregister for this? It's what we use, and
in general works really well (so well that the MJ ported it to FSL!)
chee
Hello,
This email is related to the archived “bbregister and FLAIR” email chain posted
by Kayle Sawyer on 5/23/2014
(http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36117.html).
We have also been registering with FLAIR scans, and have run into a problem
with approximately half
I'm running a monte carlo sim and am getting an error:
command line:
mri_glmfit-sim \
--glmdir MTA_persistanceCP \
--sim mc-z 1000 1.3 mc-z.negative \
--sim-sign abs --cwpvalthresh 0.999 \
--overwrite
output:
cmdline mri_glmfit --y /Studies/MTA/qdec/MTA_persistanceCP/y.mgh --fsgd
Hi Bruce,
bbregister worked very well :)
Thank you
Mohamad
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Tuesday, July 29, 2014 2:54 PM
To: Freesurfer support list
Subject: Re: [Freesurfe
I'm not sure how that could have happened. Did you run mri_glmfit
multiple times by any chance?
On 07/29/2014 03:10 PM, Jon Alan Wieser wrote:
>
>
> I'm running a monte carlo sim and am getting an error:
>
>
> command line:
>
>
> mri_glmfit-sim \
> --glmdir MTA_persistanceCP \
> --sim mc-z
I ran the analysis in qdec, not mri_glmfit . I did a few analyses in qdec
Jon
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N Greve
Sent: Tuesday, July 29, 2014 3:48 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] MR
I think that could be the problem. I don't think that qdec cleans up
after itself, so that is probably a contrast from another analysis. Try
rerunning qdec using a different output folder, or just delete that
contrast.
doug
On 07/29/2014 04:52 PM, Jon Alan Wieser wrote:
> I ran the analysis i
The current version of recon-all does not have any flexibility with
regard to bbr. I'm developing a patch that will allow this to be fixed.
Check back at the end of the week.
doug
On 07/29/2014 02:57 PM, Zamroziewicz, Marta Karolina wrote:
> Hello,
>
> This email is related to the archived “b
Hi Doug, this the command and output (here with only five subjects).
thank you!
make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg
--subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol
--template-only
make_average_surface --out myatlas.i1 --surf-reg fsaverage_s
Try adding --lh to the make_average_subject command line. Let me know if
that works and I'll change the docs
doug
On 07/29/2014 05:13 PM, angela.fav...@unipd.it wrote:
> Hi Doug, this the command and output (here with only five subjects).
> thank you!
>
> make_average_subject --out myatlas.i1 -
ERROR: Flag --lh unrecognized.
>
> Try adding --lh to the make_average_subject command line. Let me know if
> that works and I'll change the docs
> doug
>
>
> On 07/29/2014 05:13 PM, angela.fav...@unipd.it wrote:
>> Hi Doug, this the command and output (here with only five subjects).
>> thank you!
Try removing the mean from the age. By this I mean to compute the mean
age over all subjects regardless of group, then subtract the mean from
all ages.
doug
On 07/29/2014 02:39 PM, Jon Alan Wieser wrote:
>
> I'm getting the following erorr when running Qdec "Analyze"
>
> Model Factors:
>
>
> Di
Is that all it prints out? What version of FS are you using?
On 07/29/2014 05:26 PM, angela.fav...@unipd.it wrote:
> ERROR: Flag --lh unrecognized.
>
>> Try adding --lh to the make_average_subject command line. Let me know if
>> that works and I'll change the docs
>> doug
>>
>>
>> On 07/29/2014
I am using 5.3
make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg
--subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol
--template-only --lh
make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg
--subjects subj001 subj002 subj003 subj004 sub
Copy this file into $FREESURFER_HOME/bin (make a backup of the existing one)
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface
let me know if that works
doug
On 07/29/2014 05:37 PM, angela.fav...@unipd.it wrote:
> I am using 5.3
>
> make_average_subject --out mya
Hi Doug,
unfortunately the same error message appear... it looks for
rh.fsaverage_sym.sphere.reg
#@# Making rh registration template -
/Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1
mris_make_template -norot -annot aparc rh fsaverage_sym.sphere.reg subj001
subj001/xhemi su
can you send the full terminal output
On 07/29/2014 06:00 PM, angela.fav...@unipd.it wrote:
> Hi Doug,
> unfortunately the same error message appear... it looks for
> rh.fsaverage_sym.sphere.reg
>
>
> #@# Making rh registration template -
> /Users/angelafavaro/Desktop/risonanze/studyfr
ftp
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface
Connected to surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this site
220-shows implicit consent to our Acceptable Use Policy outlined at
220-http://www.nmr.mgh.harvard.
when you run make_average_subject, you will still need the --lh
doug
On 07/29/2014 06:07 PM, angela.fav...@unipd.it wrote:
> ftp
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface
> Connected to surfer.nmr.mgh.harvard.edu.
> 220-This is the Martinos Center Anonymo
I'm still not sure what is going on. I can run it with 2000 files, so I
still suspect a memory problem. Try running it with /usr/bin/time, ie,
/usr/bin/time mri_concat ...
SEnd me the last line
On 07/28/2014 03:24 PM, Isotalus, Hanna wrote:
> Dear FreeSurfer experts, Bruce/Doug,
>
> I am runn
Oh! it works now!
thank you thank you thank you
Angela
> when you run make_average_subject, you will still need the --lh
> doug
>
> On 07/29/2014 06:07 PM, angela.fav...@unipd.it wrote:
>> ftp
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface
>> Connected to su
Hello and thanks again, Bruce,
I am not sure what is going wrong here. I tried what you said and I am getting
this.
Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon- all -i -s
-sd
-all
-bash: os005a1001.nii: No such file or directory
On Jul 22, 2014, at 4:44 PM, Bruce Fischl
mailto:fis...@nmr.m
does that file exist? You don't want angle brackets <> around the name
(the angle brackets typically mean "replace this with an actual name"
cheers
Bruce
On
Wed, 30 Jul 2014, Isaiah C. Smith wrote:
Hello and thanks again, Bruce,
I am not sure what is going wrong here. I tried what you said
The command is not found.
Last login: Tue Jul 29 17:42:52 on ttys001
freesurfer-Darwin-lion-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer
FSFAST_HOME /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii
The recon-all option is no longer working and neither is the other one. I am
getting an error.
Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help
ERROR: Flag help unrecognized.
help
Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun
3 21:27:35 PDT 2014; root:xnu-2422.1
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