Hi, I have problems loading project files in QDEC.
I get the following error:
Loading data table /tmp/qdec_project_archive/qdec.table.dat...
ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat
Error loading the project file.
I would be greatful for any advice.
Best, Philipp
__
Hi Danny,
The SUBJECTS_DIR variable defines the path to a directory where freesurfer
recon data is stored for a particular study. When setting this path variable,
you don’t need to include the <> brackets.
After sourcing freesurfer, start by making a sample directory and defining your
SUBJECTS
Hi developers,
I just installed the software and there are so many problems I wish to seek
help from you when I tried “Test your freesurfer installation” on the website
Example 2
I tried several commands as follow but all failed:
1. Xues-MacBook-Air:~ DannyDeng$ export
SUBJECTS_DIR=<$FREESURF
which code. I gave 3 options below, which one did you use?
On 11/07/2017 02:43 PM, lanbo Wang wrote:
> I try to use this code to compare left and right hemisphere by paired
> t-test and add age as covariate.
>
> Thanks,
> Lanbo
>
> On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve
> mailto:gr..
Dear experts,
Do you know if there would be a mean to compare longitudinal evolution of
two vertex-wise data (i.e. kind of longitudinal correlation) with LME tools
or others ?
Best regards,
Matthieu
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard
I try to use this code to compare left and right hemisphere by paired
t-test and add age as covariate.
Thanks,
Lanbo
On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve
wrote:
> which method are you trying to implement? If #3, then you need to run
> mris_preproc separately for each subject, and t
Intensity Mean will be the mean value of the input (lGI) averaged over
the ROI.
STD, Max, Min, and Range are the intensity stddev maximimum mininum
andrange=max-min over the ROI
On 11/07/2017 12:57 PM, Buse Merve Ürgen wrote:
> Dear Freesurfers,
>
> I have two questions:
>
> 1) In the last sta
Dear Freesurfers,
I have two questions:
1) In the last stage of the recon-all -s -localGI analysis, local
gyrification index values are calculated at each pial vertices. Is there
any way (command?) to extract *vertex-wise local gyrification index values*
(of individual subjects) *before running
They might be very similar if there is not effect of genotype or the
effect is orthogonal to age.
On 10/30/2017 03:39 AM, hiroki.s...@med.tohoku.ac.jp wrote:
> Dear experts
>
> I'm using Qdec.
> I want to check regions where age and thickness are correlated, and
> regions where the thickness-age
There should be an lta file there. Are you getting an error somewhere?
On 10/30/2017 10:54 AM, Guy Avraham wrote:
> Hello Freesurfer developers,
>
> I was running FSFAST preprocessing:
>
> preproc-sess -s
> [subject]
> -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 0 -per-run
>
> The
There is not, that is not the way that FDR is used
On 11/01/2017 11:35 AM, std...@virgilio.it wrote:
> Hi,
>
> I wonder if there is a consensus to thershold the size of clusters
> obtained by FS-FAST after FDR correction?
> To cut-off clusters size>10-15 mm2 should be good? or do you advise
> m
which method are you trying to implement? If #3, then you need to run
mris_preproc separately for each subject, and then run that fscalc command
On 11/07/2017 11:33 AM, lanbo Wang wrote:
> Hi Douglas,
>
> Thanks for your reply.
> I created the fsgd file as you show me, and run code like this. Am
Hi Douglas,
Thanks for your reply.
I created the fsgd file as you show me, and run code like this. Am I right?
1.
mris_preproc --fsgd Subject.xhemi.dat \
--target fsaverage_sym --hemi lh \
--xhemi --paired-diff \
--srcsurfreg fsaverage_sym.sphere.reg \
--meas thickness \
--out lh.lh-rh.t
looks like you did not create the lta file properly. You can just pass
mris_preproc the .dat file instead of the lta.
On 11/07/2017 10:51 AM, Elisa Castaldi wrote:
> Yes, the output is in native functional space.
>
> On 7 November 2017 at 16:40, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.ed
Yes, the output is in native functional space.
On 7 November 2017 at 16:40, Douglas N Greve
wrote:
> Did you keep the spm output in native functional space?
>
>
> On 11/07/2017 09:23 AM, Elisa Castaldi wrote:
> > Yes,
> > this is what I have already done: I moved both the fsaverage and the
> > s
The difference is probably due to the partial volume correction, which
will be different with different segmentations
On 11/06/2017 03:06 PM, Ehsan Tadayon wrote:
> Thanks Bruce
> Thanks Doug
>
> that was a great help. I was able to run it as you mentioned. I also
> tried to see if I can get th
Did you keep the spm output in native functional space?
On 11/07/2017 09:23 AM, Elisa Castaldi wrote:
> Yes,
> this is what I have already done: I moved both the fsaverage and the
> subjects into SUBJECTS_DIR and the error I get is ERROR: source volume
> is neither source nor target of the regi
Hi Danny
you need to give us more information if you want us to help you. Please
include the command you ran and the entire screen output.
cheers
Bruce
On Tue, 7 Nov 2017, Danny Deng
wrote:
Dear FDs,
I encountered an odd situation:
My free surfer will always shut down when I run command
Yes,
this is what I have already done: I moved both the fsaverage and the
subjects into SUBJECTS_DIR and the error I get is ERROR: source volume is
neither source nor target of the registration.
On 7 November 2017 at 15:11, Douglas Greve
wrote:
> When you look in SUBJECTS_DIR, you should see fs
When you look in SUBJECTS_DIR, you should see fsaverage and all the
subjects being passed to mris_preproc. If not, you need to move them (or
sym link them) into that folder.
On 11/7/17 6:07 AM, Elisa Castaldi wrote:
Thanks for your answer.
If I don't specify the directory I get the following
The way that mris_preproc used to work was confusing. It made it look
like you were actually sampling to my_subject_average. In reality, it
was only using my_subject_average to perform smoothing -- the entire
analysis was done in fsaverage space. To clarify this, I required that
there by a new
I have no idea what that means. can you explain?
On 11/7/17 12:02 AM, Danny Deng wrote:
Dear FDs,
I encountered an odd situation:
My free surfer will always shut down when I run command.
My MacOS version is 10.12.6 (16G29) processor: 1.6 GHz Intel Core i5
I don’t know if the compatibility i
Dear FreeSurfer experts,
I am using mris_preproc command with following options:
mris_preproc --s s_001 --s s_002 --s s_003 --target my_subject_average
--hemi lh --meas my_input_surf.mgh --out /my_output_path/output_file
I observe mris_preproc uses mri_surf2surf. My question is related
Thanks for your answer.
If I don't specify the directory I get the following error
ERROR: cannot find fsaverage in SUBJECTS_DIR
and if I move fsaverage to SUBJECTS_DIR it says that it cannot find
manat_mp1 which is the name of the folder containing the results of recon
all for the subject sub01 (c
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