Hello,
Is it possible to save a mask of significant clusters past a certain threshold,
say 3.0, directly from the qdec interface? I want to save a few clusters, and
then map them back to individual subject space. I see I can do this if I
manually trace the cluster and save the ROI, but this not
I'm by no means an expert, but I've found that best practice dictates looking
at every subject slice by slice. This sounds daunting but I've found you can
look through a subject in 10-15 minutes.
I don't think you will get a clear answer because the quality of acquisition
can vary widely based
o
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1. savi
Hello all,
I am having an issue where the mris anatomical stats command is failing and
only printing 'segmentation fault' instead of the expected volume, area,
thickness, etc. This is happening for ~20% of the subjects, but seems to work
fine for the remaining 80%. All labels were created and ma
essed//EX03/surf/rh.white
>
>and/or view it in freeview to make sure it isn't corrupted?
>On
>Wed, 15 Jul 2015, O'Shea,Andrew wrote:
>
>> Hello all,
>> I am having an issue where the mris anatomical stats command is failing
>>and
>> only p
Hello FS-Experts,
I was wondering if there has been any work done to subdivide the thalamus
segmentation (aseg volume) into smaller sub-sections, similar to what has been
done with the hippocampus (using -hippo-subfields)? I am measuring longitudinal
changes in the volume of the thalamus from pr
Hello FS experts,
In QDEC when I click on a vertex a scatter plot is generated with each
individuals data for that vertex. Is there a simple way to extract that data
(for each subject) into spreadsheet form for a specific vertex?
-Andrew
___
Freesurfer
Hello FS experts,
I have had a continuing curiosity regarding when/what to edit in FS cortical
reconstructions. The wiki does a good job at showing how to deal with large
scale problems, (i.e. invalid tal transformation, white matter not being
recognized, large portions of the skull included in
one a number of inter-rater studies and not found any effect or
rater (all unpublished).
Sorry, as I said, I'm not sure how useful any of this is
cheers
Bruce
On Fri, 2 May 2014, O'Shea,Andrew wrote:
Hello FS experts, I have had a continuing curiosity regarding
when/what to
edit in
Hello John,
I would highly recommend you take a look at this paper
http://cds.ismrm.org/protected/11MProceedings/files/ISMRM2011-8410.pdf (Greve,
2011. An Absolute Beginner's Guide to Surface- and Voxel-
based Morphometric Analysis). I have found it to be very helpful for my
understanding.
-Andr
Hello all,
I was wondering if anyone with knowledge of the new hippocampal subfield
segmentation that is going to be released with version 6.0 could answer a quick
question. We have previously processed subjects in v5.3 and would like to use
the new hippocampal seg algorithm. How "standalone" is
Try mean centering your ICV values (I.e. Subtract the mean value from each
individual value). This has worked for me to bypass this error.
-Andrew
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of "Hirsch, Gabriella"
mailto:gabriella_hir...@meei.harvard.edu>>
Reply-To:
"frees
Gabriella
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of O'Shea,Andrew
Sent: Friday, November 13, 2015 1:55 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>;
Da
Hello all,
I was wondering if anyone with knowledge of the new hippocampal subfield
segmentation that is going to be released with version 6.0 could answer a quick
question. We have previously processed subjects in v5.3 and would like to use
the new hippocampal seg algorithm. How "standalone"
Hello,
I am trying to work through the FS-FAST tutorial on my data. I am using OSX
10.6.8 with Freesurfer v. 5.1 When I get to the make contrast command which I
run
' mkcontrast-sess -analysis test -contrast pain-v-rest -a 1 -c 0 '
I get the following output error:
" phhp-jcraggs-mb:Project ao
have matlab installed and in your path?
doug
On 07/01/2013 08:55 AM, O'Shea,Andrew wrote:
Hello,
I am trying to work through the FS-FAST tutorial on my data. I am
using OSX 10.6.8 with Freesurfer v. 5.1 When I get to the make
contrast command which I run
' mkcontrast-sess -analy
led and in your path?
doug
On 07/01/2013 08:55 AM, O'Shea,Andrew wrote:
Hello,
I am trying to work through the FS-FAST tutorial on my data. I am
using OSX 10.6.8 with Freesurfer v. 5.1 When I get to the make
contrast command which I run
' mkcontrast-sess -analysis test -contrast p
Hello,
Our data set has two T1 weighted scans for some subjects but only one for
others. Would you recommend running all subjects with no motion correction (1
scan input)? Also can files be mixed in the analysis that have had motion
correction with those who have not? Thanks!
-Andrew
___
Hello Freesurfer experts,
I am working on a study that wants to compare pre/post cortical thickness on an
intervention group and a control group. I am using FS 5.1 on a Mac. I have
processed all the recons through the longitudinal stream as described in the
wiki/tutorial. However when I go to pr
I was able to solve my problem in my earlier email included below. I downloaded
a new verison of mris_calc made it executable with chmod +x FILE and then
replaced it in the bin folder. I included this response in case anyone else
runs into the same problem and does a search.
ftp://surfer.nmr.mg
Hello,
I was wondering if I could get some clarification regarding the longitudinal
measure of rate of change in sulci depth. In our study we have a patient
population that participated in an intervention and a similar group of wait
list controls. We have scans for pre and post intervention time
Hello,
We are looking for a Post-doctoral associate with experience and skills in
multimodal neuroimaging. See below for the posting.
Post-doctoral Associate
Woods Lab, Center for Cognitive Aging and Memory
Description:
The Department of Clinical and Health Psychology and Center for Cognitive A
External Email - Use Caution
Hello,
In the past we have only used the T1 image as input for recon-all. However, we
are now also acquiring a FLAIR image and were thinking of using both for new
studies. Does anyone have any data on the differences/advantages of using FLAIR
images
with the FLAIRpial command? Any input would be greatly
appreciated. Thanks!
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of O'Shea,Andrew
Sent: Thursday, April 26, 2018 3:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Compa
Hello,
I am running into an error when using qcache. Subjects that have had manual
edits are exited with errors, while subjects that have not had edits run fine.
All subjects have had –make all ran after edits and finished without errors. I
have read about this problem and tried some of the solu
Hello all,
I was able to fix my error (see below) by re-running recon-all $SUB –autorecon2
–autorecon3 –qcache .
However I am unsure why –make all was not incorporating edits correctly? Is it
inappropriate to use –make all after manual edits? If so, should I just use
–autorecon2 –autorecon3 as a
Hello all,
Does anyone know of a toolbox/script that would automate permutation testing in
freesurfer? For example running x number of random permutations of a covariate
and recording max sig levels similar to what the software SnPM does for SPM
analyses? Thanks.
-Andrew
Hello all,
Traditionally I have only processed FS data using a single core per person, but
processing many people at once. Now we have caught up with the backlog of
scans, we have a continuos trickle of scans coming in 1 by 1. I was wondering
if anyone has tested how the speed-up of open-mp vari
External Email - Use Caution
Hello,
Would you be able to point me to the right version of the hippocampal subfield
tool as described here:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala?
The data have been processed in 6.0.0, but the stable p
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