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.thickness.00.mgh
I have 120 subjects in total and my FSGD file simply looks like this
Grou
l the best,
Anders
2015-02-21 14:42 GMT+01:00 Anders Hougaard :
> 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
Dear all,
I'm comparing cortical thickness of a group of patients to a group of controls.
I want to regress out the effects of gender, age, disease severity and
disease duration.
For the controls, the last two parameters equals zero.
When running mri_glmfit, i get ERROR: matrix is ill-conditioned
eaning your covariates. By demeaning, I mean to compute the mean
> across all subjects, then subtract the mean from all values (for each
> covariate).
> doug
>
>
>
> On 3/1/15 2:40 AM, Anders Hougaard wrote:
>
> Dear all,
>
> I'm comparing cortical thickness of
he 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.
>>
Dear experts,
I am trying to find a probabilistic map of the visual cortical area V3A.
I have not been able to find this particular area in the standard atlases
in FSL or FreeSurfer. The Jülich Histological atlas contains a V3V ROI but
not V3A.
Do any of you know have this ROI as a file or do you
(10):3911-31
>
>
> 2016-07-11 12:13 GMT+02:00 Anders Hougaard :
>
>> Dear experts,
>>
>> I am trying to find a probabilistic map of the visual cortical area V3A.
>> I have not been able to find this particular area in the standard atlases
>> in FSL or FreeS
Dear Freesurfers,
This is probably a very basic question, but I was unable to find an answer
in the mailing list:
I did a paired cortical thickness group analysis:
mris_preproc --fsgd /home/paired.fsgd --target fsaverage --hemi lh --meas
thickness --out lh.paired.00.mgh --paired-diff
(smoothing
;
> ocn.mgh is the ocn file (output cluster number), and ocn.dat will be a
> table with each input from diff.fsgd on the rows and each cluster on the
> columns
>
> On 10/6/16 2:23 AM, Anders Hougaard wrote:
>
> Dear Freesurfers,
>
> This is probably a very basic question
Excellent, thanks!
2016-10-12 20:27 GMT+02:00 Douglas N Greve :
>
>
> On 10/08/2016 02:43 AM, Anders Hougaard wrote:
> > Dear Freesurfers,
> >
> > Please see the attached image.
> > It shows inflated fsaverage surface with gamma.mgh overlaid.
> > Gamma
Dear Dr. Bock,
I get the same error in FS 5.1.0 when running recon-all -s
-label_v1.
Did you find a solution?
Best regards,
Anders Hougaard, MD
Danish Headache Center
Dept. of Neurology
Glostrup Hospital
Copenhagen
Denmark
2011/11/11 Andrew Bock
> Hello,
>
> I am having a simila
Hi Bruce,
That actually seems to do the trick. Thank you very much!
Best,
Anders
2012/6/12 Bruce Fischl
> try symlinking the ?h.white surfaces to the ?h.smoothwm and see if that
> solves your problem
>
> cheers
> Bruce
>
> On Tue, 12 Jun 2012, Anders Hougaard wrote:
>
--hemi rh
does not solve it.
Any suggestions?
Best regards,
Anders Hougaard
2011/10/18 Douglas N Greve
> The problem appears to be with the label itself. Try this conversion:
>
> mri_label2label --srclabel lh.entorhinal.label --s fsaverage --regmethod
> surfac
y running mni152reg to create a registration from
> the individual to mni152, then use that reg instead.
> doug
>
>
> On 7/4/12 5:32 AM, Anders Hougaard wrote:
>
> Dear Doug,
>
>
> I have problem similar to this:
> I am trying to convert V1 labels from the Hinds
Dear Doug,
I would like to the same thing that Kelsi (as I read the post) asked about:
For patients with a lesion in one hemisphere, I want to compare the
hemispheres with lesions to the contralateral hemispheres without lesions.
I think that your answer below is a recipe for comparing right and
Dear Freesurfers,
Is it ok to rename a subject directory, then run tkmedit and recon-all
procedures and then rename the directory back again or will this cause
problems?
All the best,
Anders
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Freesurfer@nmr.mgh.harvard.edu
h
Dear Freesurfers,
Do the anatomical input images to recon-all have to be in the same
orientation (neurological/radiological) or is it ok as long as the
orientation labels are correct?
All the best,
Anders
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Freesurfer@nmr.mgh.h
from
/Applications/freesurfer/subjects/V1_average/label/lh.v1.invivo.tif...
mrisReadTriangleFile(/Applications/freesurfer/subjects/t05/surf/lh.smoothwm):
surface doesn't match /Applications/freesurfer/subjects/t05/surf/lh.sphere
Any suggestions?
All the best,
Anders
2012/6/13 Anders Hou
Dear Freesurfers,
I would like to use V1 labels (created with the Hinds method) for a
ROI-based analysis on data analyzed with FSL FEAT using FSL featquery.
I have not run a full recon-all segmentation, only recon-all -s subjid
-label-v1
I need to convert the labels to nifti volumes while regist
Hi all,
While attempting to pre-process data for a retinotopy analysis with the
following command:
preproc-sess -surface song lhrh -fwhm 5 -sf sessid
I get the following error when motion correction is started:
Logfile is
/Users/andershougaard/Programmer/freesurfer/retinotopy/log/mc-sess01-bold
Dear freesurfers,
Which stimuli do you think provide the best retinotopic maps?
I have done a retinotopy analysis using the following stimuli:
Polar angle:
- 45 deg counter-clockwise rotating wedge
- 8 unique positions
- flickering at 2 Hz
- stimulation period: 36 sec
- no. of cycles: 6
- TR =
> the advantages of using both expanding + contracting stimuli, and the '05
> paper discusses the use of smoothly varying stimuli.)
>
> hope this helps. were you able to get reasonable looking maps with the
> stimuli you described below?
>
>
> -jon
>
>
>
>
> On
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