Dear Emma,
Thank you for your response!
Since I got this message I added the -cw256 flag:
The physical sizes are (512.00 mm, 512.00 mm, 110.00 mm), which cannot fit in
256^3 mm^3 volume.
ERROR! FOV=512.000 > 256
Include the flag -cw256 with recon-all!
However, when inspecting the orig.mgz file
Hello Freesurfer experts,
I am trying to compile FreeSurfer to make use of its CUDA capabilities. The
precompiled version does not run on my system. But when I try to compile
FreeSurfer I get the following error:
# ./configure --with-pkgs-dir=/usr/local/centos6-x86_64-packages
--enable-fermi-g
Once upon a time I had many problems with OpenGL/GLU problems in my FreeSurfer
build. Ultimately the problem was that the version of GLU installed with Mesa
package was not really compatible with the compiler that I was using. After
straightening this problem out using the configure option --
I cannot replicate this. There must be some strange permission error.
Can you try to make a new analysis with a different name and just see if
fails?
On 2/4/18 12:50 PM, Yagmur Ozdemir 19 wrote:
> Hello Dr. Greve,
>
> The analysis.info file is below. I should also say that, when I am trying to
The first frame in your input file is all 0s, so something is wrong with
the fist subject
On 2/3/18 3:03 PM, miracle ozzoude wrote:
Hello Doug,
I have uploaded the files you requested. Thank you for your help.
Best,
Paul
On Sat, Feb 3, 2018 at 1:53 PM, Douglas Greve
mailto:gr...@nmr.mgh.ha
I guess you could make the contrast [1 1 0], but I have no idea what the
interpretation would be. I'll leave that up to you
On 2/4/18 8:58 AM, std...@virgilio.it wrote:
Thanks.
what do I do if I would like to maintain the effect of "main" in the
points 2 and 3.
Best regards
Stefano
Re
On 2/4/18 10:06 AM, std...@virgilio.it wrote:
I have run:
1)
mris_preproc --fsgd GROUP1.fsgd --target fsaverage --hemi rh --meas
thickness --out rh.GROUP1.thickness.00.mgh
mri_surf2surf --hemi rh --s fsaverage --sval
rh.GROUP1.thickness.00.mgh --fwhm 10 --cortex --tval
rh.GROUP1.thickness
If you have one class and two variables, then [0 1 0] and [0 0 1]
On 2/4/18 10:23 AM, std...@virgilio.it wrote:
I would like to find where the functional connectivity is correlated
to VARIABLE 1 regressing out the VARIABLE 2.
How I should set my contrast.mtx?
Thanks
Stefano
Il 3 febbrai
You mean you want to remove everything but the WM labels? You can do it
in two steps:
1. Create a mask of the wm labels:
mri_binarize --i aparc+aseg+2mm.nii.gz --min 2999.5 --max 4035.5 --o
wm.mask.nii.gz
2. Mask the wmparc:
mri_mask aparc+aseg+2mm.nii.gz wm.mask.nii.gz aparc+aseg+2mm.maske
Thanks.
Only for I quick check of my understanding, if I'm using:
FSGD File (g1v1.fsgd)
GroupDescriptorFile 1
Title OSGM
Class Main
Variables Age
Input subject1 Main 30
Input subject2 Main 40
.
A) Contrast 1 (intercept.mtx) 1 0
B) Contrast 2 (slope.mtx) 0 1
Considering that my goa
This is the whole process output from a rerun on a subject that didn’t work the
first time or with the rerun:
Reading ctab /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab
Number of ctab entries 2
$Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $
cwd /data/user/snoli
Dr. Greve,
Yes I have tried making new files. (I also gave the previous files and folders
full permission with chmod which again didn't work) Mkanalysis-sess did not
have any problems as expected, but mkcontrast-sess failed for the same reason
of not being able to open the .config file that it
Sorry, is this related to the earlier question about how to remove
non-wm labels or is this a new submission? If a new subj, can you
describe the problem you are having?
On 02/05/2018 01:23 PM, Sims, Sara A wrote:
>
> This is the whole process output from a rerun on a subject that didn’t
> wor
The 2nd contrast (slope) is the one you want.
On 02/05/2018 01:21 PM, std...@virgilio.it wrote:
>
> Thanks.
>
> Only for I quick check of my understanding, if I'm using:
>
>
> FSGD File (g1v1.fsgd)
>
> GroupDescriptorFile 1
>
> Title OSGM
>
> Class Main
>
> Variables Age
>
> Input subject1 Main 3
I don't know, it is all very weird. What platform are you using?
On 02/05/2018 01:27 PM, Yagmur Ozdemir 19 wrote:
> Dr. Greve,
>
> Yes I have tried making new files. (I also gave the previous files and
> folders full permission with chmod which again didn't work) Mkanalysis-sess
> did not have
I obtain this error:
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir
Thickness.wls --nii.gz --fsgd g1v1_thickness.fsgd --C intercept.mtx --C
slope.mtx --pvr $SUBJECTS_DIR/rh.MCI.thickness.10B.mgh
Reading source surface /Applications/freesurfer/subjects/fsaverage/s
Dr. Greve,
I tried with root access and it still gave the same error. I am using a virtual
machine from our server that I connect with VCN, and it has freesurfer and
matlab installed and setup in its shell. The VM has Ubuntu 16.04 (Xenial),
Freesurfer v.6, and Matlab R2016b. I appreciate your h
Only fmc.odd.sm5.nii.gz is in the same dimensions as the f.nii.gz. However,
I found a flag in the selxavg3 (-no-con-ok)that I do not need to specify a
contrast. If I am not mistaken, all is good now. Thank you for your
response.
On Sat, Feb 3, 2018 at 2:03 PM, Douglas Greve
wrote:
> That file s
Try running selxavg3-sess with -monly sxa3.m
Then start matlab and run sxa3.m
On 02/05/2018 02:02 PM, Yagmur Ozdemir 19 wrote:
> Dr. Greve,
>
> I tried with root access and it still gave the same error. I am using a
> virtual machine from our server that I connect with VCN, and it has
> freesu
Dear FreeSurfer Expert,
Could you explain me what does the curvature index and folding index mean in
the Parcellation Stats File? In which way they are calculated? or you can give
me some related documents. Thanks a lot.
Ting
___
Freesurfer mailing li
I have resolve the previous error (there was a typo in the fsdg file) but
re-running I obtain this error:
Normalized matrix condition is 1
Matrix condition is 1
mghRead(/Applications/freesurfer/subjects/rh.GROUP.thickness.10B.mgh, -1):
could not open file
fsgd file is:
GroupDescriptorFile
Hello Doug,
Thank you. How do i got about fixing? Do you think it's a good idea to
start afresh on this subject (i.e. recon-all and longitudinal pipeline)?
Best,
Paul
On Mon, Feb 5, 2018 at 12:20 PM, Douglas Greve
wrote:
> The first frame in your input file is all 0s, so something is wrong wit
I don't know, you'll have to look at how you computed the first frame.
Maybe the 1st and 2nd time point for that subject are the same
On 02/05/2018 04:27 PM, miracle ozzoude wrote:
> Hello Doug,
>
> Thank you. How do i got about fixing? Do you think it's a good idea to
> start afresh on this su
Doug,
This is a new problem. I figured out my earlier issue. This makes a
8V1+aseg.mgz file there are just no 4001 and 3001's in the file so when I
binarize there is nothing there. So my question is why is it not identifying
the wm next to my label? This is happening in multiple subjects on var
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