Thank you for your answer! I already thought so, but it is good to hear it from
the expert.
Would it be correct to state (as the reviewer persistently asks for it) that it
may be somewhat informative to additionally do the voxel-wise analyses, but
that the analyses are very different resulting
Dear Richard,
Now I am getting confusion, really which version of cuda I have?. Because
when I give these command "cudadetect" nvcc -V, and cat
/usr/local/cuda/version.txt I am getting different answers.
rb@rameshbabu:~$ cudadetect
Detecting CUDA... There is 1 device supporting CUDA:
Device 0:
We are working on a longitudinal study for brain volume compartment in the
specific population. I am wondering if there are any longitudinal brain
volume data for normal patients? I saw some studies using ADNI normal data
as reference, but cannot find them.
thanks!
Lawrence
Emory University
__
The ROI vs voxel-wise differences can come from a lot of places. When
you do an ROI analysis, you get a lot of averaging so the noise can be
expected to be much less than voxel-wise. If your effect is largely
constrained to an ROI, then the ROI result will be more powerful. But
they are really
I think you may have sent this reply to me by accident. I just want to make
sure the person that actually asked the question gets the reply.
Thanks,
Valerie
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Z K
Sent: Tuesday, May 23, 2017 3:04:56 PM
Thanks so much for the speedy response,
Using the export command you recommended didn't give me any problems.
However, I've downloaded the new version, but when following the steps for set
up the terminal is still trying to use the old fsfast file path:
[vbecker@bhfilbey ~]$ export FREESURFER_
The reason the mri_convert command failed is because the 'cp' command
before it failed. Please make sure you copy the
'$FREESURFER_HOME/subjects/sample-001.mgz' file into what ever directory
you are currently in before executing the 'mri_convert' command. This is
done as follows:
cp $FREESU
Postdoctoral Position at Boston/Children’s Hospital & Harvard Medical School
The GaabLab (gaablab.com) at the Laboratories of Cognitive
Neuroscience at Boston Children’s Hospital/Harvard Medical School invites
applications for a post-doctoral associate position in the area of
developmental cogn
Hi Valerie,
It looks like you might be using bash shell, in which case you should be
using the 'export' command instead of setenv to change its value (note
the difference in syntax):
export SUBJECTS_DIR=
Please note... It looks like you are using a very old version of
freesurfer. Freesurfe
Hi FreeSurfer Developers,
I'm new to Linux as well as freesurfer and picking up with the program where an
old lab assistant left off. He already installed the program and fsfast, but
set the subjects directory using a file path unique to his user and I'm having
trouble changing it. Calling up
Hi,
I'm using FS v6.0 stable. Is there any difference between running recon-all
with -autorecon2-wm or -autorecon-noaseg? It looks like both are starting at
-normalization2 and running through the rest of autorecon2 with no changes to
inputs/args compared to "regular" -autorecon2.
Is this true
I know what was wrong . My run folders are not zero-padded strings!
Thank you for the hint!
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Tuesday, May 23, 2017 11:46 AM
To: freesurfer@nmr.
Version 6
On Tue, May 23, 2017 at 11:40 AM, Douglas N Greve wrote:
> And is this version 6 or 5.3?
>
>
> On 05/23/2017 08:21 AM, miracle ozzoude wrote:
> > Hello Bruce,
> > So far, I have only encountered this error in 2/147 of my subjects.
> > Best,
> > Paul
> >
> > On Mon, May 22, 2017 at 11:0
What was your preproc-sess command and what folder are you running it
from? And did you use 3-digit, zero-padded strings as your run folder?
On 05/23/2017 09:17 AM, Alshikho, Mohamad J. wrote:
>
> Hi Doug,
>
> I want to analyze rsfMRI data using FS-FAST. Kindly, I have question
> regarding the
Dear Dr. Mak,
Thank you for your time and response! I looked into the link you suggested.
Unfortunately, it’s not exactly what I need, although I realize my question may
have been stated incorrectly.
Part of the rationale behind creating the map(s) is to be able to see if the
findings we repor
And is this version 6 or 5.3?
On 05/23/2017 08:21 AM, miracle ozzoude wrote:
> Hello Bruce,
> So far, I have only encountered this error in 2/147 of my subjects.
> Best,
> Paul
>
> On Mon, May 22, 2017 at 11:00 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Paul, are
sure, if you upload I'll take a look
cheers
Bruce
On Tue, 23 May 2017, Falk Lüsebrink
wrote:
Dear all,
I’m processing native 250 µm T1-weighted MPRAGE data with v6. I downsampled
the data gradually from 250 µm to 1 mm and am processing it with the -hires
flag, openmp and expert options
Hi Sabrina
that isn't a defect - the surface is topologically correct. It is a
pretty big triangle though, which is surprising. We need to investigate
some things in fsaverage anyway and will look into this
cheers
Bruce
On Tue, 23 May 2017, Sabrina Brigadoi wrote:
Dear FreeSurfer experts,
Hi Doug,
I want to analyze rsfMRI data using FS-FAST. Kindly, I have question regarding
the command “ preproc-sess / Freesurfer v6”
In order to begin the analysis, I followed the steps as in FS-FAST wiki. First,
I organized the tree folders for the project as
“study_folder/session_ID/bold/run”.
Hello Bruce,
So far, I have only encountered this error in 2/147 of my subjects.
Best,
Paul
On Mon, May 22, 2017 at 11:00 AM, Douglas N Greve wrote:
> Hi Paul, are you using version 6? Is this happening on more than one
> subject or is this subject an outlier?
>
>
>
> On 05/19/2017 10:28 AM, Bru
No, I am working with MATLAB on the outputs of freesurfer and the
freesurfer_surf2voxels command is under MATLAB. I want to check the
coordinates of lgi values found by recon - all lgi command on MATLAB. When
I check the coordinates on the brain image I realize a shift app 5-10 vox
according to re
Dear Experts,
I am having some trouble with the display of the area in Freesurfer/Qdec.
In particular, after running the analysis, I can see some results in the
terminal but in the display section of Qdec, no areas are shown.
I have tried to wait or re-launch the analysis but the result was
On 23 May 2017 at 01:13, Ramesh Babu wrote:
> Ok. I will try cuda 8.0 and let you know the result. Should I install cuda 5
> before installing cuda 8? or Can I run both?
You'll only be able to have one version of the CUDA driver, but you
should be able to have multiple CUDA SDKs.
Richard
__
On 23 May 2017 at 01:10, Ramesh Babu wrote:
> I have one question. When use -use-gpu flag, can I use -itkthreads 8 or -use
> openmp 8 flag?
That's not something I've tested. I think that OpenMP at least is OK
(things will run in parallel on the CPU or the GPU.
Richard
__
Hi Siri,
Are you trying to overlay the p value associated with each region on the
fsaverage surface? This may help:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50465.html
Best Wishes,
Elijah
Dr. Elijah Mak, Research Associate
Department of Psychiatry, Old Age Psychiatry Gro
Dear Freesurfer experts,
I haven't had the pleasure of receiving a response (yet), and was wondering
whether that is because more information is needed?
In addition to the general theoretical question, the second part of the
question is as important to me: Is there is any way, known to you expe
Hi Livia,
I am not very familiar with the paired analysis (never used it and did
not develop it). From a glance (others may know better) your files look
OK, the first creates the paired differences, the second is for the
group comparison to test if the group mean of the paired differences
di
Hi Lisa,
there are big differences in the cross sectional stream (see release
notes). Most of these affect the longitudinal stream directly. Regarding
the longitudinal pipelines, there are no big changes to the pipeline,
but as lots of the cross sectionally processed results and tools from
th
Hi Gregory,
If looking at longitudinal changes, I would use uncorrected ROI
volumes. You could consider including ICV as a covariate (for offset
and slope interaction, to test if ICV has an effect on your slopes).
Best, Martin
On 05/19/2017 04:44 PM, Gregory Book wrote:
In writing a paper
Hi Matthieu,
Y = b0 + b1 tij + b2 si + b3 si * tij
(Y thickness, b0 intercept, b1 slope, b2 score, b3 score effect on
slope, where t_ij is the time of subject i at time point j, s_i is
subject score)
= (b0 + b2 si) + (b1 + b3 si) tij
so the slope is made up of (b1 + b3 si), a global comp
Hi Doug,
I have used fscalc to create subject-level Z score maps of cortical thickness
against a set of healthy controls.
fscalc $i/surf/lh.fsaverage.mgh sub
group_mean_control_lh.mgh div group_std_control_lh.mgh --o
$i/surf/lh.Z.thickness.fsaverage.mgh; done
Beyond this, is there a way to adj
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