Hello Freesurfers,
I am trying to run QDEC for a longitudinal analysis.
I've run the command "long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out ./qdec/cross.qdec.table.dat" to adjust my qdec table to the right format for QDEC (with only one line / subject).
I've also created the
Thanks Doug.
Any suggestions for a more appropriate design?
I guess this is a common situation where two or more parameters only
apply to one group (in this case patients) and are zero or constant in
the other.
Best,
Anders
2015-03-02 21:21 GMT+01:00 Douglas N Greve :
>
> It looks like the 4th co
Hi Doug,
thank you very much for your answer!
Am 02.03.2015 um 11:30 schrieb Douglas N Greve :
>
> You would do the long analysis using a random effects analysis.
OK, so basically do 2-stage modeling
(https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), right?
> For each sub
Hi Bishesh,
it is a know bug. in your recon-all find this block (should be in line
6148)
if ( ! $found_tpNid ) then
echo "ERROR: $tpNid is not in
${longbasedir}/${BaseSubjsListFname}"
echo ""
exit 1
endif
and replace the first line (if statemen
Hi Rick, in the future please post to the list and not to us personally.
Thanks! When you did the volume-based analysis, it should have masked
out anything anything that was not subcortical. Did it not? If not, then
when you run mri_glmfit you can add --mask
$SUBJECTS_DIR/fsaverage/mri.2mm/bra
It looks like the 4th column is always -0.9 and the 6th col is always
-9.138 which makes them redundant with column 2 and causes the error.
doug
On 03/02/2015 03:16 PM, Anders Hougaard wrote:
> Dear Doug,
>
> Thanks for the answer. I deliberately chose not to demean.
> With demeaning I get the s
Dear Doug,
Thanks for the answer. I deliberately chose not to demean.
With demeaning I get the same error (see below). Any suggestions?
Best,
Anders
Design matrix --
1.000 0.000 -0.600 0.000 17.137 0.000;
1.000 0.000 -0.800 0.000 11.962 0.000;
1.000 0.000
r-values are not produced. The coefficients are regression coefficients,
not correlation coefficients. If you want correlation coefficinets, I
would do it in matlab. download this
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit_pcc.m
copy it to $FREESURFER_HOME/matlab
On 03/02/2015 04:04 AM, Matthieu Vanhoutte wrote:
> Dear Doug,
>
> Thank you for helping !
>
> Yes I directly used the regheader option because in the steps before I
> already registered ASL maps on anatomical T1.
>
> The brain.fsaverage.lh.mgh come from the projection of the T1 brain
> mask (di
On 02/26/2015 01:46 PM, Janosch Linkersdörfer wrote:
> Hi all,
>
> I experimented with the different flags for mri_surfcluster and have 2 issues
> that I don't understand, it would be great if somebody could enlighten me:
>
> 1) When I set --thmin (or --fdr) with --thsign abs, I get what I would
It looks like you'll want to use mri_mask (?)
doug
On 02/26/2015 10:12 AM, Sarah Finnegan wrote:
> Hi Bruce
>
> Thanks for your reply,
> I did use mri_vol2surf for the sampling
>
> mri_vol2surf --src {zstat1} --srcreg {anat2exf.register.dat} --hemi
> {hemi}--projfrac {0.8} --out {out file name}
try this
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/lta_convert
On 02/26/2015 12:48 PM, Xiaomin Yue wrote:
> Hi,
>
> Is it possible to download lta_convert?
>
> Thanks,
>
> Xiaomin
>
>
>
>
> On Thu, Feb 26, 2015 at 9:35 AM -0800, "David Grayson"
> mailto:dgray...@ucdavis.edu>>
Hi Chris, the error was very unpredicatable. If you want to see whether
it was wrong or not, you can look at the contrast matrix it created
(C.dat in the contrast folder).
doug
On 02/25/2015 07:11 AM, Christoph Abé wrote:
> Hello,
>
> I am dealing again with the "old" issue of using DOSS in QDE
You would do the long analysis using a random effects analysis. For each
subject you can get a slope (this won't work if the subject only has 1
time point), then concatenate the slopes into a file and run mri_glmfit,
then follow the procedures from the archive email you reference.
doug
On 02/2
You can use $SUBJECTS_DIR/fsaverage/mri/aparc+aseg.mgz (already in the
volume), then use mri_label2vol (with --seg flag) and
$FREESURFER_HOME/average/mni152.register.dat for the registration. The
problem is that the cortical labels are all very thin and won't
intersect well with your ICA volum
It will just recreate the files, no need to delete anything.
doug
On 02/23/2015 10:25 AM, Anne Park wrote:
> Hello,
>
> I had a question about using the -qcache command for smoothing.
> Previously, the -qcache command was used on several subjects in my
> dataset, and since then, these subjects
Can you use mri_surfcluster to do this? It can output a binary mask,
annotation, or label. You just need to give it the input and a
threshold. If you just want constrain it to a given label, then you'll
need to create a mask.
doug
On 02/20/2015 09:14 PM, Eric Reavis wrote:
> Hello Freesurfers,
That is strange. Can you send the full terminal output from the first
call to mri_glmfit-sim?
doug
On 02/23/2015 03:49 AM, Eiran Vadim Harel wrote:
> Hello Freesurfers,
>
> I use freesurfer v5.3.0
>
> When I do group analysis correction for multiple comparisons for lh as
> follows:
>
> mri_glmf
Can you send your fsgd file?
On 02/21/2015 08:42 AM, Anders Hougaard wrote:
> Dear Freesurfers,
>
> Sorry for this newbie question:
> I'm preparing my data for a group analysis using mris_preproc:
>
> mris_preproc --fsgd nocov.fsgd --target fsaverage --hemi lh --meas
> thickness --out lh.nocov.thi
What do you mean that no surfaces were generated? There are two things
you have to do. One is to create the template. The second is to apply
the template (the first set of steps).
doug
On 02/20/2015 04:15 AM, pfannmo...@uni-greifswald.de wrote:
> Hi FSexperts,
>
> I would like to compute a symm
On 02/18/2015 09:54 PM, Xiaomin Yue wrote:
> Hi Doug,
>
> Thanks for your response. I did run bbregister to register the EPI to
> T1, but it did not resample the EPI to T1 space, just generated a
> register.dof6.dat file, which is expected according to the help
> document. Also, the help docu
I'm not sure what is going on there. Can you send me the cluster.summary
file?
doug
On 02/18/2015 02:47 PM, Hirsch, Gabriella wrote:
>
> Yes – sorry this is probably easier with images.
>
> The files I’m visualizing are the sig.mgh (uncorrected) and
> cache.th13.abs.sig.ocn. mgh (cluster correc
The log file you sent has a different error:
ERROR: cannot find allVfix in NMASA_induction.lh
On 02/17/2015 01:40 PM, Joseph Andreano wrote:
> Hi Doug,
>
> We're having difficulty extracting signal from ROIs using
> funcroi-table-sess. Every time we try, we get the following error
> message: "
it if's a T1-weighted flash that should work
cheers
Bruce
On Mon, 2 Mar 2015, Satrajit
Ghosh wrote:
hi bruce,
we are missing a T1 scan from a participant. is there any pathway in
freesurfer to reconstruct from the T2-flair/flash scan?
cheers,
satra
___
Yes, I think I fixed it.
On Mar 2, 2015, at 11:21 AM, Douglas N Greve wrote:
>
> I know that Ruopeng was fixing it a few months ago. Ruopeng, did you finish
> that fix?
> doug
>
> On 03/02/2015 10:28 AM, Xiaomin Yue wrote:
>> Hi Doug,
>>
>> thanks for your response. You are right that the f
I know that Ruopeng was fixing it a few months ago. Ruopeng, did you
finish that fix?
doug
On 03/02/2015 10:28 AM, Xiaomin Yue wrote:
> Hi Doug,
>
> thanks for your response. You are right that the freeview in v5.3
> doesn't generate the registration file correctly. However, the newest
> deve
Hi,
while trying to get a nifti phasemap projected on a surface vie rtview I run
into the problem that the overlay has the wrong orientation on the surface.
Loading on overlay: setting the "Registration" to "Calculate identity matrix",
loading a identity matrix as
registration file didn't have a
hi bruce,
we are missing a T1 scan from a participant. is there any pathway in
freesurfer to reconstruct from the T2-flair/flash scan?
cheers,
satra
___
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Hi Doug,
thanks for your response. You are right that the freeview in v5.3 doesn't
generate the registration file correctly. However, the newest development
version of freeview can generate a lta registration file correctly with correct
source and target volume. then, a registration file in
Hello Siddharth,
the following manual describes all the steps needed to flip phase encoding
direction on the MR 750 : http://fmri.ucsd.edu/download/DTItopup_manual.pdf
. Good luck!
Marcel
2015-02-25 18:28 GMT+01:00 Siddharth Srivastava :
> Hi Everyone,
> In order to introduce distortion cor
Hi Amy,
Good point. You can first use mri_vol2vol to upsample to 1mm:
mri_vol2vol --mov yourROIs.nii --targ
$FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --regheader --o
yourROIs_1mm.nii --interp nearest
then
mri_vol2surf --mov yourROIs_1mm.nii --mni152reg --hemi rh --surf white
--o rh.ROIs.
hi, of course. The result look strange too. Please see the attached file
with -mni152reg command and this transformation matrix is not for the 2mm
resolution image. lets me know if you have any other suggestion. thanks.
Amy
On Mon, Mar 2, 2015 at 12:26 PM, Thomas Yeo wrote:
> Hi Amy,
>
> Have
Hi Amy,
Have you tried the "--mni152reg" flag instead of "--reg
/usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat". Is the
attached picture from your original command or mni152reg flag?
p.s. Can you please reply all to the freesurfer list?
Cheers,
Thomas
On Mon, Mar 2, 2015 at 6:54 P
Dear Freesurfers,
I am trying to display the regional regresssion coefficent for age in qdec.
However the colorbar still gives me the traditional 0, 1.3 etc
is there anyway to change the colorbar. I would like to be able to display
only regions that have more than say 0.3 correlation with age - s
Dear Doug,
Thank you for helping !
Yes I directly used the regheader option because in the steps before I
already registered ASL maps on anatomical T1.
The brain.fsaverage.lh.mgh come from the projection of the T1 brain mask
(dilated by 1) on the fsaverage.
1) So isn't it better to project firs
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