Hi,
I’ve run across the following error while trying to run qdec in my linux 64 bit
computer,
qdec.bin: error while loading shared libraries: libtiff.so.3: cannot open
shared object file: No such file or directory
Is there any specific file that I need to download or change configuration of?
Dear all,
I am trying to measure the volume of the dorsolateral prefrontal cortex
in a large group of subjects. I have created a new label that only
includes the dlpfc for a subject but realised that the same label file
cannot be used on another subject. Has anyone created a customised ROI
f
p; Raz et al 1999 :Psychol
Aging. 14(3):436-44
Prapti
-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Saturday, 7 February 2009 5:29 AM
To: Prapti Gautam
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] creating label for dlpfc
How are you
Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
Sent: Friday, 6 February 2009 3:47 PM
To: Prapti Gautam
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] creating label for dlpfc
Prapti,
You can use mri_label2label to do that, something like:
mri_label2label --srclabel rh.your_dlpfc.lab
Yes, the labels are in the subjects' label directories; putting the full
path to the labels solved the problem. Thank you,
Prapti
-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Thursday, 12 February 2009 8:39 AM
To: Prapti Gautam
Cc: Nick Schm
Dear all,
I've come across a similar problem to the one described before in qdec,
but cannot find a solution for it,
I've previously visualised my data using qdec, but when I tried to run
it again I get the following error. I've checked to make sure my subject
is named correctly and I am in the
Deleting 'qdec/Untitled' worked! Thanks,
Prapti
-Original Message-
From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu]
Sent: Thursday, 5 March 2009 11:10 AM
To: Prapti Gautam
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] qdec error in analyze
Prapti,
Try de
Dear Freesurfers,
Is there a reliable way to measure sulcal widths from T1 images using
Freeesurfer? I have found information on sulcal curvatures and depth but
not on width measurement and am wondering if it is possible to do so.
Thanks,
Prapti
Dear all,
I am trying to measure local Gyrification Index in my subjects and can't
get started. I get the following error:
Flag -localGI not recognised
I have Matlab and its Image processing toolbox installed in my computer
and am running freesurfer version 4.0.2. Do I have to have the
Dear Freesurfers,
I ran a monte carlo simulation for thickness analyses using mri_glmfit
and found new files in the contrast subdirectory. I was able to figure
out what the first two represent, but was wondering if any one could
clarify what information the rest of the files show:
mc-z.nega
Dear Freesurfers,
I just have some quick questions regarding qdec:
1. How many covariates does the latest version of qdec allow you to
select? I am using FS version 4.3.0 and I cannot select more than 2
continuous variables. I am just wondering if a newer version allows you
to selec
your help,
Prapti
-Original Message-
From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu]
Sent: Friday, 10 July 2009 4:15 AM
To: Prapti Gautam
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] qdec question
The newest version of FreeSurfer does not contain any changes
Dear freesurfers,
I have a problem running localGI in one subject. I previously got an
error message that said that one of the vertex value was aberrantly
high. The mris euler number on the subject was fine - but I relaunched
the recon-all -autorecon2 -autorecon3 for the hemisphere in questi
Hi Marie,
I'm using version 4.3.1. I've relaunched recon-all -all for the
hemisphere, hopefully this will solve the problem,
Thanks,
Prapti
-Original Message-
From: Marie Schaer [mailto:marie.sch...@unige.ch]
Sent: Thursday, 22 October 2009 9:54 PM
To: Prapti Gautam
Cc:
Dear Freesurfers,
I have a question regarding thickness analyses using mri_glmfit. I am
interested in correlating cognitive performance with a specific region
in the brain and to increase the power of my analyses I want to conduct
mri_glmfit on only my ROI. I was just wondering if it is possib
Dear FreeSurfers,
Is there a way to extract thickness values for individual subjects for a
vertex that are obtained after analyses with mri_glmfit? I have seen a
script that does this with qdec - but most of the analyses I run are on
mri_glmfit, so was wondering if the script on the user contri
Hi,
Is it possible to run recon-all so that both control point edits and
brain volumes can be processed with a single command?
Currently I use
recon-all -autorecon2-cp -autorecon3 -subjid
for corrections to control points
and
recon-all -autorecon2-pial -autorecon3 -subjid
for corrections to
Dear FreeSurfers,
I am having some problems creating a label in tksurfer and subsequently
converting it into a volume file. I have created a custom label in a
test subject using tksurfer which loads correctly onto the surface when
viewed with tksurfer. However, when I load the label into tkmedi
Dear all,
Reposting the following question again,
Thanks,
To: freesurfer@nmr.mgh.harvard.edu
Subject: labels don't match with tkmedit and tksurfer
Dear FreeSurfers,
I am having some problems creating a label in tksurfer and subsequently
converting it into a volume file. I hav
Dear FreeSurfers,
I am trying to convert an Analyze object map (saved as a set of .img
/.hdr files) where I've traced ROIs so that I can load them as labels or
overlays in FreeSurfer. Has anybody done this before? What would be the
best way to proceed?
Thanks,
Prapti
___
Hi,
I'm trying to use orient_mri to orient a volume that is displaying as an
axial rather than a coronal volume. According to the instructions, I
need to see 4 views and be able to rotate the loaded volume - but I only
see one window.. do you know why this is ? there wasn't a error message
as s
Dear freesurfers,
I am trying to convert a label that I have hand drawn into tksurfer into
a volume file using mri_label2volume and succeed in transforming into a
volume file but the volume looks splotchy and the ends are not connected
, i.e. instead of a smooth bit of cortex I get disjoi
an I merge the annot files created from each hemisphere so that I can
pass it to mri_aparc2aseg?
Thanks,
Prapti
-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Thursday, 16 September 2010 1:34 AM
To: Prapti Gautam
Cc: freesurfer@nmr.mgh.harvard.edu
S
hemispheres. Do I
then edit these files ? where exactly do I use mri_binarize?
Thanks,
Prapti
-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Friday, 17 September 2010 12:44 AM
To: Prapti Gautam
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer
dear all,
I am trying to extract the mean values of lgi from the cortex from a group of
subjects. I found the following command useful in extracting for one subject:
mris_anatomical_stats -mgz -f lh.lgi.stats -b -a aparc.annot -c
lh.lgi.annot.ctab -t pial_lgi $SUBJECT lh
However, I have a lot
Hi,
I want to copy a label I've created on a region on the left hemisphere to the
right (or vice versa) and was wondering if there has been any progress on the
tools avaialable. Is there perhaps a beta version of the functionality that
could be used?
Thanks,
Prapti
Dear freesurfers,
I am trying to convert a surface label into a volume file so that it can
subsequently be viewed as a 3-D model. To create the label I've
followed the steps from
http://www.ci.uchicago.edu/wiki/bin/view/HNL/EditROI and have thus
edited my color table LUT file.
The command I a
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