Hi VM,
They can stay all in the same .csv file. The "fwep" files will have
p-values corrected across all columns of this input.
All the best,
Anderson
On 2 February 2017 at 12:09, neuroimage analyst <
neuroimage.anal...@gmail.com> wrote:
> Thanks, Anderson. If there are several other measures
Why are you passing a dicom file as the registration file? The reg file
is a FS-specific text file used to store the registration matrix.
On 2/2/17 6:35 PM, Anderson Napolitano wrote:
Hello Experts!
I am having trouble running the following command:
tkregisterfv --mov
/Users/djsandoval/
I have tested a recon-all -all CPU and GPU with and without the -hires option
and everything seems to run fine. So at the moment they seem to be compatible
or at least the GPU version doesn't crash. So that is ok.
Thanks for your time.
Dr Chris Adamson
Research Officer, Developmental Imaging, M
On 1 February 2017 at 22:07, Chris Adamson wrote:
> I understand they are not a priority. But are they compatible with the CPU
> versions? Should we be using the CUDA versions if they aren't guaranteed to
> be up-to-date?
I haven't run any comparisons against the CPU binaries recently. And
if
Strange, that fixed things right up for me. You might make sure you know
where you are calling FreeSurfer from and that there are no old license
files lying around.
Peace,
Matt.
From: on behalf of Anthony Dick
Reply-To: Freesurfer support list
Date: Thursday, February 2, 2017 at 5:46 PM
T
Thanks Matt. I already tried it with a new registration, but it doesn't
hurt to try it again. That may be where the issue is. I'll post if that
turns out to be the problem. Thanks!
Anthony
On 2/2/17 6:28 PM, Matt Glasser wrote:
Like I said, they changed the format at some point and stopped
a
Hello Experts!
I am having trouble running the following command:
tkregisterfv --mov
/Users/djsandoval/Desktop/Selwyn/M87151031-2016002/Followup/PETCT/PET/STATICBRAINPET/2016002B/IM-0001-0001.dcm
--reg
/Users/djsandoval/Desktop/Selwyn/M87151031-2016002/Followup/PETCT/PET/STATICBRAINPET/2016
Like I said, they changed the format at some point and stopped accepting the
old format with FS 6.0. I have used FreeSurfer for a long time too and
found that I had to get a new license file with this version.
Peace,
Matt.
From: on behalf of Anthony Dick
Reply-To: Freesurfer support list
D
Hello,
I have used my old file, registered under two different emails (and
received the code and made new files each time, named both .license and
license.txt). Restarted the computer etc. I am wondering if it is a
permissions issue. It seems to be finding the file where I put it. Have
never
Hi Joe
there are slight differences, and for sure we reserve the right to use
the knowledge that it is a FLAIR scan in the algorithms, so you should
probably rerun
cheers
Bruce
On Thu, 2 Feb 2017, Joe Necus (PGR) wrote:
>
> Hello,
>
>
> I am running recon-all on the latest version of freesu
It will behave differently as some of the parameters change depending
upon whether it is a T2 or FLAIR. This will only affect the surface creation
On 02/02/2017 05:19 PM, Joe Necus (PGR) wrote:
>
> Hello,
>
>
> I am running recon-all on the latest version of freesurfer (Version 6)
> and would l
Hello,
I am running recon-all on the latest version of freesurfer (Version 6) and
would like to know whether there is any difference between using the -T2
-T2Pial and -Flair flags.
I am currently running recon-all with a T1 and FLAIR image, but have used the
-T2 -T2pial flags and would like
The second design is fine if there is no significant interaction between
1 or 2 and 3. You'll have to create the design matrix yourself or you
can create an fsgd file with 7 classes
On 02/02/2017 11:38 AM, Tim Reess wrote:
>
> Dear Freesurfer experts,
>
> I would like to set up a design matrix
So ismac.m is not defined in your matlab implementation? What version of
matlab are you using? What kind of computer are you running on?
On 02/02/2017 01:48 PM, aral ahmadi wrote:
>
> Dear experts
>
> I have a question regarding Freesurfer- LGI error I got during running
> LGI after all recon s
I don't think there is anything really wrong. There are computation
limits on the maximum significance. When the given voxel goes beyond
that, I set it to this ridiculously high level. This high level just
means that it is really significant.
On 02/02/2017 12:18 PM, Rodriguez-Thompson, Anais w
Sorry, which labels are consistent and which are inconsistent?
On 02/02/2017 02:52 PM, Levman, Jacob wrote:
>
> Hi there,
>
>
> I've been conducting an asymmetry analysis based on FreeSurfer
> measurements. There are regions of the brain with known left-right
> asymmetry such as BA44 which exhi
The .license that it comes with is not the same as the license.txt that you
have to acquire. I was able to use an old license.txt from my Freesurfer
5.3 for 6.0.
Best
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Thu, Feb 2, 2017 at 3:21 PM, X K
Try checking your recon all.log in your scripts folder of the subject.
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology
On Thu, Feb 2, 2017 at 1:52 PM, shi yao wang
wrote:
> Dear FS experts:
> How to check recon-all finished without any error?
> Some
Thanks Dr. Fischl. I will surely give a try to this.
On Wed, Feb 1, 2017 at 3:17 PM, Bruce Fischl
wrote:
> I see. Have you run recon-all on each hemi? If so, use bbregister to
> register the surfaces to the fmri data, then use mri_vol2surf to map the
> activations on to the left and right surfac
Hi Martin,
I dropped --generic-time flag as you suggested in the previous e-mail and run
the long_stats_slopes command again like this:
long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat --stats
aseg.stats --meas volume --sd $SUBJECTS_DIR --do-rate --do-pc1fit --do-pc1
--do-
Richard,
I understand they are not a priority. But are they compatible with the CPU
versions? Should we be using the CUDA versions if they aren't guaranteed to be
up-to-date?
Dr Chris Adamson
Research Officer, Developmental Imaging, Murdoch Childrens Research Institute
Murdoch Childrens Researc
Hi,
We extracted volume measures from 7 ROIs in 2 groups and compared
a) Mean of each ROI volume between group, and compared independently such
as
i) whether mean of ROI 1 in group 1 is equal to mean of ROI1 in group 2
ii)whether mean of ROI 2 in group 1 is equal to mean of ROI2 in group 2
and so
Hi Freesurfers,
Thank you for the help you provide through this list.
Is there a way to get, for each vertex, the identify (or thickness values)
of the surrounding vertices in a 10mm radius? The command mris_convert has
the '-v' option, but that produces only 5-6 vertices and there is no option
t
They updated the format so you have to get another.
Peace,
Matt.
On 2/2/17, 2:13 PM, "Anthony Dick" wrote:
>Hello,
>
>I have been using Freesurfer for a number of years, and just installed
>v6.0. I run into this problem:
>
>--
try to rename the file to license.txt?
On Thu, Feb 2, 2017 at 9:13 PM, Anthony Dick wrote:
> Hello,
>
> I have been using Freesurfer for a number of years, and just installed
> v6.0. I run into this problem:
>
> --
> ERROR:
Hello,
I have been using Freesurfer for a number of years, and just installed
v6.0. I run into this problem:
--
ERROR: Invalid FreeSurfer license key found in license file
/Applications/freesurfer/.license
If you are out
Hi there,
I've been conducting an asymmetry analysis based on FreeSurfer measurements.
There are regions of the brain with known left-right asymmetry such as BA44
which exhibits strong leftward asymmetry (the left side is bigger than the
right). This is accurately reflected when you compare th
Dear FS experts:
when I running hippocampus subfield, I got error messages:" Cannot find CTF
archive".
I copied command and screen to you.
Thank you very much!
[silun.wang@node5 N01]$ *recon-all -s N01 -hippocampal-subfields-T1*
Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20160611-876a0e6
Dear FS experts:
How to check recon-all finished without any error?
Sometime, there are showing no error message, however, when I running
hippocampus subfield, it does not run.
thanks
Lawrence
Emory
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.
Dear experts
I have a question regarding Freesurfer- LGI error I got during running LGI
after all recon steps been ran with no problem. you could see the error
below.
*reading filled volume...*
*??? undefined function or variable 'ismac'.*
*error in -->load_mgh at 68*
*if(strcmp(computer,'MAC'
Dear experts,
I have a question regarding Freesurfer- LGI error I got during running LGI
after all recon steps been ran with no problem. Attached you could see the
error.
The error is ...Undefined function or variable 'ismac' - matlab is
expecting that variable to be defined (it's trying to detec
Dear Freesurfer experts,
I would like to set up a design matrix for a design that is not
QDEC-able. I have three categorical factors:
1.disease status: 2 levels
2.gender: 2 levels
3.scan site: 4 levels
The first design I set up was the following (the rows are just for
illustration and don’
Thanks, Anderson. If there are several other measures such as volume,
thickness, FA, can I then put them in a single csv file and run the
command or I have to create 3 csv files, one each for volume, thickness,and
FA and also invoke -corrmod?
Thanks
Regards
VM
On Feb 2, 2017 1:01 AM, "Anderson
Hi VM,
Please see below:
On 1 February 2017 at 02:38, neuroimage analyst <
neuroimage.anal...@gmail.com> wrote:
> Hi,
>
> We extracted volume measures from 7 ROIs in 2 groups and compared
> a) Mean of each ROI volume between group, and compared independently such
> as
> i) whether mean of ROI 1
Thanks again — it was a huge help!
On 31 Jan 2017, at 18:25, Yendiki, Anastasia
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Barbara – Thank you for your kind words. As you’ve read, if the output files
are generated, then you’re good to go. Bedpost does not differentiate between
longitudinal an
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