What version are you using? I fix a problem last Sept that might be like
this. I've put a new version of mri_label2vol here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.linux
Try this and let me know if it works.
doug
On 6/1/12 10:46 PM, Leon wrote:
Hi, Bruce
Hi, Bruce
Here are my two command lines
For transferring the annot from the source template to the target subject:
/home/freesurfer/bin/mri_surf2surf --srcsubject ${srcsubject} --sval-annot
rh.ic2.annot --trgsubject ${trgsubject} --trgsurfval src_2_trg.annot --hemi rh
--surfreg sphere.reg0
W
Can you send us your command lines and screen output?
On Jun 1, 2012, at 7:44 PM, Leon wrote:
> Hi, folks
>
> when I transferred the annotation file obtained using
> mri_make_face_parcellation based on ic2 (162 labels) to a volume file using
> mri_label2vol, I found that one ROI patch was m
Hi Jeff,
that should not happen. Are you certain this time point is from the same
subject?
You are using version 5.1 I assume?
Try to open the longitudinal time points on top of each other (e.g. in
freeview) to see how well aligned they are.
Also load the surfaces from the base to see if the fit
Hi Cindy, :
1. did you check the individual labels to make sure they landed in about
the right place?
2. do not use smoothing for this
Also, you'll probably want to work on the stack of data in fsaverage
space. This file is called y.mgh and it is created when QDEC runs. You
can extract the dat
you probably need to redo them since it didn't find the cortex.label it
will include the zero thicknesses in the medial wall for example
On Fri, 1
Jun 2012, mdkrue...@uwalumni.com wrote:
Actually one last question-
I used label2label to transfer some labels and grab ROI thickness averages fro
I see. So you must have overwritten it with something, maybe a stats
file. You'll need to rerun mris_make_surfaces or autorecon 3 for that
subject/hemi to recreate it.
cheers
Bruce
On Fri, 1 Jun 2012, mdkrue...@uwalumni.com
wrote:
> Bruce-
>
> It is, and i agree, for instance here is the lh.co
That is not possible. If you mask out everything you don't want, you can
run it with --projfrac-max to get the maximum along the normal. Since
stuff out of the ribbon is 0, it will give you stuff in the ribbon. This
is a little messy though because it won't necessarily give you the point
closes
Hi Doug,
I was wondering if it was possible to have the intensity at the nearest
non-zero voxel projected onto the vertex.
Perhaps if we use --projfrac 0.5, mri_vol2surf will select mostly GM
voxels, which is our goal.
Thanks,
Kate
On 06/01/2012 12:47 PM, Douglas N Greve wrote:
>What do you me
that makes sense. also just for clarification to a point a made before - i
was not using label2label to transfer the rh.cortex.label we have been
discussing across subjects, i was transferring other labels, which is most
likely why the label2label and measurements didnt fail. I believe i
misunderst
not unless you are trying to visualize the label
On 06/01/2012 01:16 PM, mdkrue...@uwalumni.com wrote:
> Thanks, i am also still able to display the rh in tksurfer without
> issue, shouldnt that also fail with the current rh.cortex.label?
>
> michael
>
> On Fri, Jun 1, 2012 at 11:57 AM, Douglas N
Thanks, i am also still able to display the rh in tksurfer without issue,
shouldnt that also fail with the current rh.cortex.label?
michael
On Fri, Jun 1, 2012 at 11:57 AM, Douglas N Greve
wrote:
> I would have expected that to fail. You can check the time stamps to see
> if your output is newer
I would have expected that to fail. You can check the time stamps to see
if your output is newer or older than rh.cortex.label. If older, it is
probably ok.
On 06/01/2012 12:53 PM, mdkrue...@uwalumni.com wrote:
> Actually one last question-
>
> I used label2label to transfer some labels and grab
Actually one last question-
I used label2label to transfer some labels and grab ROI thickness averages
from the labels on the subject with the rh.cortex.label that has been
overwritten. I received no errors during this, does this mean that the
label transfers and averages are valid, or do i need t
What do you mean ignore? If you mask them out of the volume so that they
are 0 (or -999), then they will be 0 or -999 in the output.
doug
On 06/01/2012 12:25 PM, Derin J Cobia wrote:
> Bump.
>
> I'm interested in the answer to this question as well. Doug/Bruce, do
> you know?
>
> -Derin
>
>
> On
Bump.
I'm interested in the answer to this question as well. Doug/Bruce, do you know?
-Derin
On May 29, 2012, at 8:43 PM, Kathryn I. Alpert wrote:
Dear Freesufer experts,
I am wondering if it is possible to tell mri_vol2surf to ignore certain voxels
in the src volume, for instance, by settin
Hi, Bruce
Thank you very much for your information and the codes.
Best
Leon
From: Bruce Fischl
To: Leon
Sent: Friday, June 1, 2012 10:48 AM
Subject: Re: [Freesurfer] transfer annot files from template to each subject
p.s. here's a gzipped version of mris
Doug -
That does indeed seem to be the problem! Ill just rerun some things here to
rectify that. Thanks for all the help everyone!
Best-
Michael
On Fri, Jun 1, 2012 at 11:01 AM, Douglas N Greve
wrote:
> I think the label file got overwritten at some point. Check the time
> stamp and see if it i
When you use --regheader, then it uses the vox2ras transform in the
header. If you pass it a register.dat file as input, then vox2ras is
ignored.
doug
On 05/31/2012 06:39 PM, Shay Ohayon wrote:
> Hi,
>
> Bump?
>
> Can someone please explain to me the puzzle described below regarding
> tkregiste
I think the label file got overwritten at some point. Check the time
stamp and see if it is much different than the other rh files
On 06/01/2012 11:55 AM, mdkrue...@uwalumni.com wrote:
> Bruce-
>
> It is, and i agree, for instance here is the lh.cortex.label file
>
> #label , from subject ??
> 14
Doug-
INPUT
mri_surf2surf --hemi rh --s UNM_SUPERSAMPLE --sval rh.meth.00.mgh
--fwhm 10 --cortex --tval rh.meth.10.mgh
OUTPUT
srcsubject = UNM_SUPERSAMPLE
srcval = rh.meth.00.mgh
srctype=
trgsubject = UNM_SUPERSAMPLE
trgval = rh.meth.10.mgh
trgtype=
srcsurfreg = sphere.reg
trgs
Bruce-
It is, and i agree, for instance here is the lh.cortex.label file
#label , from subject ??
149955
22 -10.374 55.016 3.203 0.00
112 -6.294 36.386 -7.809 0.00
114 -6.137 38.556 13.808 0.00
247 -11.304 45.214 -2.709 0.00
248 -6.278 39.973 2.192 0
what is your full command line and terminal output?
doug
On 06/01/2012 11:49 AM, Bruce Fischl wrote:
> that is the rh.cortex.label file? It doesn't look like it
>
> On Fri, 1 Jun 2012, mdkrue...@uwalumni.com
> wrote:
>
>> Bruce-
>>
>> Here you go. Subjects recoded.
>>
>> Graph: name
>>
>> Dat
that is the rh.cortex.label file? It doesn't look like it
On Fri, 1 Jun 2012, mdkrue...@uwalumni.com
wrote:
> Bruce-
>
> Here you go. Subjects recoded.
>
> Graph: name
>
> Data: path
> Variable: Subject
> Measurement: external
> subject id, class id, variable value, measurement value, stand
Bruce-
Here you go. Subjects recoded.
Graph: name
Data: path
Variable: Subject
Measurement: external
subject id, class id, variable value, measurement value, standard deviation
S1 Cl1 0.0 3.10522500831 0.268702566292
S2 Cl1 1.0 2.67585065105 0.396833961125
S3 Cl1 2.0 3.07631433273
It should let you do that. Can you send me the qdec table file?
doug
On 05/31/2012 12:11 PM, Laura M. Tully wrote:
> Hi,
>
> I am using freesurfer 5.1.0 and qdec 1.4. I'm interested in looking at
> between group differences in thickness in relation to two other
> continuous measures whilst contr
Hi Diane
you need to symlink the directories
$FREESURFER_HOME/subjects/lh.EC_average
$FREESURFER_HOME/subjects/rh.EC_average
$FREESURFER_HOME/subjects/V1_average
$FREESURFER_HOME/subjects/fsaverage
in your SUBJECTS_DIR
cheers
Bruce
On Fri, 1 Jun 2012, Diana Omigie wrote:
I am getting an e
Hi Michael
can you check to see that your partition is not full? Does the
rh.cortex.label file exist in that subject's label dir? If so, what are the
first couple of lines?
cheers
Bruce
On Fri, 1 Jun 2012,
mdkrue...@uwalumni.com wrote:
To anyone who can help -
I am trying to tun a GLM on
To anyone who can help -
I am trying to tun a GLM on a set of data and am currently receiving an
error during the mri_surf2surf portion. When running this portion i receive
an error ( could not scan # of lines from (path to rh.cortex.label)). This
does not happen when running this portion for the
if you use ?h.sphere it will generate a parcellation this is uniform in
subject space, if you use sphere.reg it will generate one that is uniform
in fsaverage space (and in which the parcels can be compared across
subjects). They are *not* anatomical though, in the sense that the aparcs
corresp
Doug,
thank you very much.
One subject result from mris_preproc only have partial brain data. this
caused error. But I dont know why this subject data failed in
mris_preproc.
my command is the following,
mris_preproc --target fsaverage --hemi $hemi --out sub1.mgh --paired-diff
--iv subj1.run1_cop
I am getting an error during the recon all step that I cannot figure out.
It seems to occur in the stage where labels are being written as two
label files are missing in the labels directory (
lh.entorhinal_exvivo.label and lh.entorhinal_exvivo.label ) and an error
log message emerges in the lab
Post-doc
position within
the Collaborative Research Centre 940 "Volition and Cognitive
Control: Mechanisms, Modulators, and Dysfunctions" at
the Department
of Child and Adolescent Psychiatry, University Hospital C. G. Carus,
Dresden University of Technology
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