I heard from Koen a while back that a new improved version was in the works. I
have
several projects I would be interested in using it for. Any info on timelines
for release
or a publication ?
thank You
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Dear Doug and Freesurfers,
I noticed that the DOSS option no longer exists in qdec and that Doug said
there was a bug related to it.
If i want to assess the differences in cortical thickness between groups
while covariating for age and gender, since i don't expect any
interactions, can i just demea
Hello,
Any help how to make qdec.table.dat file will be highly appreciated.
Thanks
Best Regards,
Muhammad
Naveed Iqbal Qureshi
Ph.D. Candidate
Bio-Medical Signal & System Analysis Laboratory
Department of Medical System Engineering
Gwangju Institute of Sciences and Technology
123, Cheomdan
Hi everyone,
I want to analyze with DOSS the relationship between performance on a
cognitive task (called '15wt') and cortical thickness, in one group,
controlling for the effects for age, gender and education. As a
Freesurfer-newbie, it be would really great if someone could check my .sfgd
file a
Do you want to transfer them to fsaverage space or to the individual
anatomical space?
doug
On 10/04/2013 01:42 AM, Ruth Carper wrote:
> Hi,
> I'd like to take some masks that I have in MNI standard space in FSL
> and map them to Freesurfer surface space. The goal is to extract
> measures of
Yes, though I would probably use [0 0 1 0 0] instead of .5. They will
give you identical p-values. Using 1 instead of .5 makes the beta value
(ie, regresssion coefficient) more interpretable (if that is something
you will look at).
doug
On 10/04/2013 07:50 AM, Anita van Loenhoud wrote:
> Hi ev
Have you looked atthe qdec tutorial?
On 10/04/2013 05:41 AM, Muhammad Naveed Iqbal Qureshi wrote:
>
> Hello,
>
> Any help how to make qdec.table.dat file will be highly appreciated.
>
> Thanks
>
> *Best Regards,*
> *Muhammad Naveed Iqbal Qureshi*
> Ph.D. Candidate
> Bio-Medical Signal & System Ana
Demeaning will not turn a DODS into a DOSS.
On 10/04/2013 04:48 AM, Erik Lindberg wrote:
> Dear Doug and Freesurfers,
> I noticed that the DOSS option no longer exists in qdec and that Doug
> said there was a bug related to it.
> If i want to assess the differences in cortical thickness betwee
I'm trying to apply voxel deletions made to the brainmask.mgz to the wm.mgz. As
I understand it, if I run
mri_copy_values brainmask.mgz 0 wm.mgz
all of the 0 value voxels, or the deleted voxels in braibmask.mgz will be
applied to the wm.mgz (provided they have the same geometry or some such).
Hello Freesurfer experts,
I am having difficulty when trying to extract LGI values from a specific label
I made. mris_anatomical seems to work when I run it with an annotation, so I am
not sure why I am having this error.
mris_anatomical_stats -l sub200/label/lh.precuneus.label -t
sub200/surf/
Hi Doug,
I guess it boils down to the question how to get a group PCC map after a
RFX GLM?
Using -m PCC seems to only give me a map per subject. Are you calculating
PCC from the t- values? Thanks,
Caspar
On Thursday, October 3, 2013, Caspar M. Schwiedrzik wrote:
> Hi Doug,
>
> On Thursday, Octob
Hi Everyone,
I am having trouble running mris_anatomical_stats on an annotation file
produced from my group analysis in qdec.
This is my code, but it seems to want to pull the annotation file from the
subject/label directory. Should I just make a copy into everyone's label file?
mris_anatomic
I think you are conflating the 1st level and the 2nd level. You could
get pcc out of the 2nd level regardless of what you are using for the
input from the first level. I've attached a matlab script that will
compute the pcc for mri_glmfit output
doug
On 10/04/2013 03:33 PM, Caspar M. Schwied
Hi,
I am trying to calculate whole-brain mean cortical thickness in each
individual subject for correction of regional mean thicknesses.
I see on the wiki that this is recommended to be done by:
bh.thickness = (lh.thickness X lh.area) + (rh.thickness X rh.area) /
(lh.area +rh.area)
In my table I se
Hi Doug,
thank you very much for sending the Matlab function. When I run this, it
creates a pcc.mgh file for my osgm contrast. However, the values seem
strange. They range from -630 to 36 for my particular dataset.
I was expecting something between -1 and 1.
Caspar
2013/10/4 Douglas N Greve
> I
how long have you waited?
On Fri, 4 Oct 2013, Marcos Martins da Silva wrote:
Hi, Freesurfers
I am getting some interesting hippocampal surfaces with the following steps:
1- recon-all -all -hippo-subfields
2- mri-concat (only CA1, CA23, CA4DG and the tail complement volumes)
3- a custom OCTAVE
Dear FreeSurfer Experts,
Is there a way to estimate the SNR in MPRAGE scans besides using wm-anat-snr ?
For examples, I read that SNR is improved in multiecho MPRAGE and I am
wondering how that is computed?
Thanks!
Daniel
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F
That command works. Thanks so much, Martin!
Best,
Tricia
From: Martin Reuter
To: Tricia Merkley
Cc: Freesurfer list
Sent: Thursday, October 3, 2013 9:48 AM
Subject: Re: [Freesurfer] LGI longitudinal data
Hi Tricia,
try
recon-all -long subject001 subje
Can you tar up you glmfit dir and drop it to me on our file drop?
On 10/04/2013 05:29 PM, Caspar M. Schwiedrzik wrote:
> Hi Doug,
> thank you very much for sending the Matlab function. When I run this,
> it creates a pcc.mgh file for my osgm contrast. However, the values
> seem strange. They ran
you can do something like this
cd $SUBJECTS_DIR/$subject
mri_segstats --slabel $subject lh label/lh.cortex.label --i
surf/lh.thickness --id 1 --sum stats/lh.meanthickness.dat
On 10/04/2013 05:22 PM, Mollie Bayda wrote:
> Hi,
> I am trying to calculate whole-brain mean cortical thickness in ea
This may sound incredibly trivial, but try putting a "./" infront of
qdec, ie, "-a ./qdec/..."
doug
On 10/04/2013 03:42 PM, Tara Ann Miskovich wrote:
> Hi Everyone,
>
> I am having trouble running mris_anatomical_stats on an annotation file
> produced from my group analysis in qdec.
>
> This
Done. Thank you very much for looking into this.
Caspar
2013/10/4 Douglas N Greve
> Can you tar up you glmfit dir and drop it to me on our file drop?
>
>
> On 10/04/2013 05:29 PM, Caspar M. Schwiedrzik wrote:
>
>> Hi Doug,
>>
>> thank you very much for sending the Matlab function. When I run th
Hi Tara
if you upload the subject we will track it down
cheers
Bruce
On Fri, 4 Oct 2013, Tara Ann
Miskovich wrote:
> Hello Freesurfer experts,
>
> I am having difficulty when trying to extract LGI values from a specific
> label I made. mris_anatomical seems to work when I run it with an annota
Hi Jon
voxels deleted with tkmedit are set to 1, not 0, so try that
Bruce
On Fri, 4 Oct 2013, Jonathan Holt wrote:
> I'm trying to apply voxel deletions made to the brainmask.mgz to the wm.mgz.
> As I understand it, if I run
>
> mri_copy_values brainmask.mgz 0 wm.mgz
>
> all of the 0 value voxe
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