Hi Cesar, you can run
mris_convert lh.white lh.white.asc
to convert to ascii. Each vertex is in MNI305 space. Is that good
enough? There is a matlab script by Matthew Brett that attempts to
convert to Tal coords. You could easily convert to MNI152 as well.
doug
On 6/24/13 4:34 PM, Cesar
Hi Rotem - No problem. Were these scans by any chance acquired with a
coronal slice prescription? In the axial views that you sent, the artifact
that you're pointing to looks like misalignment between consecutive
coronal slices, which could be due to head motion.
a.y
On Tue, 25 Jun 2013, Ro
Sorry, can't open the image.
On Sun, 23 Jun 2013, Rotem Saar wrote:
Hi there,
Long time:). Well I wrote to the list several times regarding high FA values
I got when performing DTI analysis.
Today we know that the problem was an additional direction (we had 17
directions instead of 16 - we us
Dear Bruce,
Thank you very much!
Sincerely,
Ye
On Mon, Jun 24, 2013 at 7:32 PM, Bruce Fischl wrote:
> Hi Ye,
>
> you would never have two files, as each file represents one image, or
> slice from a sequence. So you might have two sequences of files, say
> Barba001-1.img, Barba001-2.img... Bar
Hi Ye,
you would never have two files, as each file represents one image, or
slice from a sequence. So you might have two sequences of files, say
Barba001-1.img, Barba001-2.img... Barba001-256.ima, and Baraba002-1.ima,
Barba002-2.ima Barba002-256.ima. Then you would use -i twice, once wit
Dear Bruce,
Thank you very much for your suggestion, but I am afraid that I still don't
quite understand you.
In order to make it simple, suppose I have two files, Barba001.IMA and
Barba002.IMA, coming directly from the scanner.
Now if I enter *recon-all -s Barba -i Barba001.IMA* from the comm
Hi Ye
you only need to give it a single file from each run and it will find the
rest. The only time you use -i more than once is if you acquired more
than 1 T1-weighted volume. Definitely don't give it all the files that
make up the same volume
cheers
Bruce
On Mon, 24 Jun 2013, ye tian wrote
Dear David,
I wonder whether there is a short cut for recon-all -s Barbara -i
/path_to_data/scan1.dicom -i /path_to_data/scan2.dicom ... -i
/path_to_data/scan100.dicom
Recon-all -i takes only a single file as an input. A typical user, however,
has hundreds of files for a particular subject. For e
June 13, 2013 (repost to Freesurfer list June 24, 2013)
The Human Connectome Project (HCP) WU-Minn consortium is pleased to
announce our second quarterly (Q2) release of HCP image and behavioral data.
What’s in the HCP Q2 data release? The Q2 data include multimodal MRI and
behavioral data collec
Hi Mike
the 3.5-4mm thickness probably makes them not usable since it means
opposing banks of a sulcus will be in the same voxel pretty frequently
sorry
Bruce
On
Mon, 24 Jun 2013, Michael Kranz wrote:
Hi all,
I'm having trouble determining whether or not to use our T2 images for the
new p
Hi all,
I'm having trouble determining whether or not to use our T2 images for the
new pial refinement feature. *Most importantly, I'm wondering if our T2
image parameters are sufficient for the T2 pial refinement. The parameters
of our T2 images are as follows:*
T2 TSE overlay with a voxel size
Dear Zoe,
have you checked whether all directories within your subject directory
correspond to subjects which have been reconed with the -hippo-subfields
flag?
Cheers,
/Eugenio
On 06/24/2013 04:00 PM, Yang, Zoe wrote:
Hi all,
I am getting error messages while running
kvlQuantifyHippocampal
Hello,
Anyone know of a fast way to get the talairach coordinates of a vertex
index in fsaverage. A function or script is best since I want to do this
for a large number of vertices.
Thank you for any help you guys can provide.
Cesar
___
Freesurfer mail
Hi Bruce,
So technically speaking I guess I have three different brain
atlases for neonates, 1 yr olds, and 2 yr olds. Each atlas contains a set
of 3D images made up of the intensity model, tissue probability maps, and
anatomical parcellation map. I obtained these from a study done by UNC
Hi Mark
can you clarify what you mean? What template are you referring to?
Bruec
On Mon,
24 Jun 2013, Mark Plantz wrote:
Hello freesurfers,
I am currently attempting to create my own .tiff templates for a
series of infant fMRI's (neonates, 1 yr olds, and 2 yr olds). I currently
have th
Hi all,
I am getting error messages while running
kvlQuantifyHippocampalSubfieldSegmentations.sh, similar to the error mentioned
in an earlier email
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg24430.html). We
did use the -hippo-subfields flag for all of our subjects first, an
Hello freesurfers,
I am currently attempting to create my own .tiff templates for a
series of infant fMRI's (neonates, 1 yr olds, and 2 yr olds). I currently
have the templates in .nii.gz, .mgz, and .img/.hdr formats.
Is there any easy way to convert from one of these formats to a .tiff ima
Dear Koen,
Freeview returns 8 lines of the error message "invalid drawable" whenever
executed. The messages are as follows
2013-06-24 14:24:57.930 Freeview[1937:303] invalid drawable
2013-06-24 14:24:57.931 Freeview[1937:303] invalid drawable
2013-06-24 14:24:57.944 Freeview[1937:303] invalid dra
Hi,
I am examining the affect a metal artifact has on fMRI data, and I am
using Eccentricity mapping with the retinotopy analysis in FSFast. I
was recently asked to switch from examining the difference in the fsig
to examining the difference in the betas. I opened up beta.nii.gz and
I can see that
Hello Freesurfer users,
I'd hope to know the RESEL number in my group GLM analysis data.
I can calculate the number of vertices and also see the fwhm.dat in the
ouput GLM folder, but I wonder if there is anyway of finding out RESEL size
if freesurfer also provides that info like SPM does.
-Glen
___
Hi Nick and Doug,
Can you suggest an alternative way if QDEC is unable to handle a single group?
I would like to run these analyses to address reviewers comments.
Best,
Manish
From: Douglas Greve
To: Manish Dalwani
Cc: "freesurfer@nmr.mgh.harvard.edu"
Dear FreeSurfers
I'm using Freesurfer 5.1 on Ubuntu 12.04 LTS.
Currently running paired analysis as described here
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
After
mri_glmfit \
--glmdir lh.paired-diff \
--y lh.paired-diff.thickness.sm05.mgh \
--fsgd paired-diff.fsgd \
--C mean.
Hi Cathy
If you only have three groups in your
data (Control subjects, High risk patients, Ill patients) then you should drop
the
“Controls versus all others and controls*time interaction” terms
from your design matrix. Otherwise it is ill-conditioned. One way to
check your design matrix is b
Dear Freesurfer,
I have checked the mail list, none could answer my problem.
I added up the value of all vertxes in the .area or .area.pial files, find that
brain size did not contribute much to that vertex-sum. However, some experiment
used total brain volume as a regreesion coefficien
Dear Freesurfer experts, I am currently trying to do a cortical
thickness group analysis with one factor, three levels . I have run
mri_preproc and mri_surf2surf, and am now trying to run
mri_glmfit --y lh.group.thickness.10B.mgh --fsgd easy2.file --C
contrast1.mtx --surf fsaverage lh --cort
Sorry for the delay. I'm new to FSL, Freesurfer, and VB, so maybe I'm doing
it wrong, but I have the impression I cannot run FSL from the VB:
- Typing 'fsl' yields 'fsl: Command not found'.
- Checking the environment with 'echo $FSLDIR' yields 'FSLDIR: undefined
variable'
- Checking the path with '
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