Hello Freesurfer Team,
Sorry for being so late with this message I was trying different things to
accomplish extracting BOLD values from a flattened surface. I followed the
overall instructions on this website
http://web.mit.edu/fsl_v5.0.8/fsl/doc/wiki/FreeSurfer.html. I have the
flattened patch f
Hi Kristina - You can enter nifti DWI volumes in the configuration file
(or any other format that mri_convert can recognize). You should do the
entire processing from scratch (including bedpost) using the concatenated
data.
Best,
a.y
On Fri, 20 May 2016, Kristina Jelinkova wrote:
> Hi Anasta
Hi Anastasia,
Thank you for your response. Yes, we have created the concatenated DWIs and
bvec/bval files that we have gotten after running each of the sequences
separately from trac-all. How can we run these concatenated nii.gz mages
through the ball-and-stick model fit (I'm assuming the confi
Hi Kristina - I'm assuming the 2 data sets were acquired in the same
session and with the same acquisition parameters, other than the b-values?
Then you can just concatenate the DWIs from the 2 runs (e.g. with
mri_concat) and also concatenate the b-value and gradient vector tables
(and make s
Hi,
I'm trying to get some cortical thickness volumes for an ROI that I have
(I'm pretty much following the instructions at
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness verbatim),
but for some of my subjects I'm getting errors that look like this when I run
mdi_seg
Hi Anri - The FA values are extracted in the native space of each subject,
which is why those are the only coordinates that you see. If you want to
display the results of your analysis on an average path, after running
trac-all -stat, you can use the stats/*.path.mean.txt files (see also the
Hi Qi - Is /Studies/*/DTI/dmrirc_subject a single file or multiple files?
What are the contents of that file?
a.y
On Fri, 6 May 2016, Zeng, Qi wrote:
Hi,ย
I am running dti data with trac-all. I followed the command:
trac-all -prep -c /Studies/*/DTI/dmrirc_subject
but it exited with erro
Hi Elijah - Since the error occurs in the CST, is any of the brainstem cut
off for this subject? It's hard to tell from the screenshot, but the field
of view seems a bit cropped inferiorly.
Best,
a.y
On Thu, 5 May 2016, Elijah Mak wrote:
> Dear Anastasia Yendiki,
> I ran into a hitch while ru
Hi Xiaofu - It's hard to tell but it looks like the brain mask (which
comes from the structural data) is a bit too large in the temporal lobe,
so it's possible that the structural-to-diffusion registration didn't go
so well for this subject. You can check on this by overlaying the
structural
Hi Peggy - If it looks like a single path, it definitely is an
initialization error. If you reinitialize repeatedly and it doesn't get
fixed, it might be that something went wrong earlier in the processing
(for example some part of brain that the tract goes through is missing
from the brain m
Hi Marissa - If your bvecs/bvals files are in row format, you need to make
sure that you have the most recent update that supports this. It was a
feature that was added later on:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
Best,
a.y
On Fri, 15 Apr 2016, Marissa Pifer wrote:
H
Hi Elijah - Are the bvec/bval files located in the current directory from
where you are running trac-all? This is where it seems to be looking for
them:
cp 16084.bvec
/Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvecs
cp 16084.bval
/Users/MacPro/Documen
Hello all,
I had a question regarding the program Tracula. I have two different DTI
sequences that I wish to run (b=900 and b=2000) but am unsure at which step I
am suppose to merge the two sequences together.
At this point, I have pre-processed each of the sequences separately using
trac-al
Excellent, thank you! To do that, do I send an e-mail to the listserv with the
log files attached or do I use the filedrop?
yea, can you post the log file of both the successful and failing runs?
On 05/19/2016 11:28 AM, Aloi, Joseph wrote:
>
> Hi Doug,
>
> No thatโs not how I usually store my
mri_label2label --srclabel rhrh.label --srcsubject fsaverage --trgsubject SUBJ
--trglabel SUBJ_rhrh --regmethod surface --hemi rh
does not produce output.
Suggestions are very wellcome.
Thanks
Stefano
>Messaggio originale
>Da: std...@virgilio.it
>Data: 20-mag-2016 19.51
>A:
>Ogg: [
label2label and label2vol are options?
mri_label2label --srclabel ROI.label --srcsubject fsaverage --trgsubject
Control61 --trglabel prova.label --hemi rh --regmethod surface
I have tried the command line above ma the mask output is miss registered
Stefano
>Messaggio originale
>Da:
The Translational Research Center for TBI and Stress Disorders (TRACTS) at VA
Boston Healthcare invites applications for two positions as Postdoctoral
Research Associate in brain imaging of Veterans.
The TRACTS conducts a prospective longitudinal cohort study and has recruited
over 500 Veterans
Hi Jason
SMS/multi-band doesn't really help 3D sequences. I believe we have done
ipat=3 and it has been fine, but perhaps Andre (or someone else who has
gotten this type of data) can confirm?
cheers
Bruce
On Fri, 20 May 2016, Jason Tourville wrote:
Hello freesurfer experts,
Do you have a
I'm just following up on this e-mail. I have not heard anything yet.
-Tim
On Mon, May 9, 2016 at 3:16 PM, Timothy Hendrickson
wrote:
> Free Surfer Support,
>
> I have been using the command line version for group analysis since my
> data set has too many factors for QDEC.
>
> There are a few th
Hello freesurfer experts,
Do you have a recommended "optimal" T1 protocol on Bay 1 for cortical
reconstruction?
For the past couple years, we've been using the 'tf1_mgh_multiecho_1mm_iso"
protocol which has PAT = 2 and a TA = 6:02. ๔๔
I'm wondering if a faster option at the same resolution is no
Hi Martin,
Thank you for the feedback. Our version of FS 5.3 is the centos4 build
(which works perfectly) so I downloaded the same when got a copy of dev
(nightly build 05-11-16). However, I just tried the centos6 and the
brainstem module now works smoothly (including mri_robust_register).
There
Hello,
I've got a very basic question related to group analysis. If I want run a
correlation of voxels in the cortex with a variable *controlling *for
another continous variable, how do I do this. I know how to run them both
in a GLM simultaneously by coding the matrix 0 1 1, however, how do I loo
sure, that should work
cheers
Bruce
On Fri, 20 May 2016, std...@virgilio.it wrote:
Specifically, I have a .label from tksurfer and I would like to report this
label on subj orig.nii.gz
Messaggio originale
Da: std...@virgilio.it
Data: 20-mag-2016 10.36
A:
Specifically, I have a .label from tksurfer and I would like to report this
label on subj orig.nii.gz
Messaggio originale
Da: std...@virgilio.it
Data: 20-mag-2016 10.36
A:
Ogg: [Freesurfer] MASK.label from fsaverage to volume in subject space
Hi list,
to trasform a MASK.label (
Hi list,
to trasform a MASK.label (created by tk surfer) from surface to volume is
correct to use:
1. mri_surf2surf to register the mask from fsaverage to subj space2.
mri_surf2vol to report the label (subj space) to volume (subj space)
Thanks.
Stefano___
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