Dear Freesurfer Mailing List,
I wish to run a GLM in freesurfer with 3 categorical variables
(haplotype-2levels, gender-2levels, group-2levels), and 1 continuous
variables (age). Unfortunately, the MRI images I am using come from five
different testing sites, so I also need to account for the
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Yea, that should work. Use the filedrop at the end of this email
On 10/23/2014 04:13 PM, Flavin, John wrote:
> We only have a few examples of the multi frame dicom, and they’re all
> of humans. We can anonymize one and email it to you directly.
>
> Flavin
>
>> On Oct 23, 2014, at 1:18 PM, Douglas
We only have a few examples of the multi frame dicom, and they’re all of
humans. We can anonymize one and email it to you directly.
Flavin
On Oct 23, 2014, at 1:18 PM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>> wrote:
I doubt that it will work. I've never actually seen a multi-frame d
yes
On 10/23/2014 02:48 PM, dgw wrote:
> If I have events which precede the first MR volume, can I input
> negative values in my par file?
>
> I understand my power, and the advantage of doing this will be
> minimal, but I wanted to inquire if FS-FAST is capable of handling
> this case.
>
> Thanks,
Hi Alex,
you are not looking at a "one sample group mean" (osgd) so don't pass
that flag. Your design is probably something like
1 A other_co_vars_to_regress_out
(these are column vectors).
so contrast in that case would be [ 0 1 0... ]
That should create all outputs. All of this is really cr
If I have events which precede the first MR volume, can I input
negative values in my par file?
I understand my power, and the advantage of doing this will be
minimal, but I wanted to inquire if FS-FAST is capable of handling
this case.
Thanks,
Dan
___
Hi Martin,
thanks for confirming. I duplicated the parameter and got good results in qdec.
I also tried to repeat the analysis with mri_glmfit but I can't manage to come
to an end.In order to analyse the correlation between pc1 and parameter 'A', it
seems that I have to construct an fsgd file, th
I doubt that it will work. I've never actually seen a multi-frame dicom
myself. Can you upload one to me? It should be of a phantom, not a
human, so we can avoid privacy issues.
doug
On 10/23/2014 01:07 PM, Flavin, John wrote:
>
>> Hi Timothy
>>
>> you should be able to. You can use the -nth
Hi Timothy
you should be able to. You can use the -nth switch to convert
each frame individually
cheers
Bruce
On Mon, 11 Jul 2011, Timothy Brown wrote:
> Hi All,
>
> Can mri_convert be used with multiframe dicom?
Is this advice still valid? I tried converting a multi frame DICOM (176 fra
you may need to add some control points
On Thu, 23 Oct 2014, Corinna Bauer
wrote:
> We actually ran it through the processing stream and only the middle of the
> brain made it into the wm.mgz and the surfaces.
>
> On Thu, Oct 23, 2014 at 12:49 PM, Bruce Fischl
> wrote:
> Hi Corinna
>
>
We actually ran it through the processing stream and only the middle of the
brain made it into the wm.mgz and the surfaces.
On Thu, Oct 23, 2014 at 12:49 PM, Bruce Fischl
wrote:
> Hi Corinna
>
> it's hard to say. It's quite noisy, but you should give it a try
>
> Bruce
> On Thu, 23
> Oct 2014, C
Hi Corinna
it's hard to say. It's quite noisy, but you should give it a try
Bruce
On Thu, 23
Oct 2014, Corinna Bauer wrote:
> Hello,
> I am analysing some structural data for collaborators and one of the
> datasets has a strange artefact in it. Is there any way to adjust for the
> intensity ban
Thanks
On Thu, Oct 23, 2014 at 12:34 PM, Douglas N Greve wrote:
>
> In theory that works, but remember the FS total cranial volume is only
> an estimate based on the talairach transform. It is not counting voxels
> that are inside the skull.
>
> On 10/23/2014 12:30 PM, Mohammed Goryawala wrote:
In theory that works, but remember the FS total cranial volume is only
an estimate based on the talairach transform. It is not counting voxels
that are inside the skull.
On 10/23/2014 12:30 PM, Mohammed Goryawala wrote:
> Thanks Doug.
>
> I was looking at a paper "ARANGO, C., MCMAHON, R. P., LE
Thanks Doug.
I was looking at a paper "ARANGO, C., MCMAHON, R. P., LEFKOWITZ, D. M.,
PEARLSON, G., KIRKPATRICK, B. & BUCHANAN, R. W. 2008. Patterns of cranial,
brain and sulcal CSF volumes in male and female deficit and nondeficit
patients with schizophrenia. Psychiatry Research: Neuroimaging, 16
No, not currently. This is quite a hard problem even if you have a T2.
The pulse sequences are usually low enough bandwidth that fat from the
scalp and skull marrow shift into the CSF spaces making it impossible to
properly segment that area as CSF. If you wanted an approximate value,
you coul
I tried to run a recon-all on a brand new subject and ran into the same issue,
so I just moved the subjects directory on a hunch. I'm used to running
Freesurfer on a CentOS system, so I'd never really considered OSX being as
picky as it seems to be about write permissions. Bert's recon has been
Interesting. Ive never encountered that issue before but Ive also never
conducted an install test on subject bert on Mavericks or Yosemite. Ill
take a look. Thanks for the update.
-Zeke
On 10/23/2014 12:03 PM, Matthew Riddle wrote:
> Hi Zeke,
>
> So I may have solved the issue. Since /applicati
You can use mri_annotation2label to break up the annotation into
individual labels, then use mris_label2annot to recombine selected
labels into an annotation or use mri_merge_label to merge them into a
single label. All you have to do is decide with labels define prefontal
doug
On 10/23/2014
Hi Zeke,
So I may have solved the issue. Since /applications is write protected by
default, I had to run the recon-all with sudo. But it seems like the
subroutines of recon-all don't inherit the permissions, so I moved my Subjects
directory to Documents, and then I can run recon-all without the
It is just a text file, so you can just look in it. You can also run
aparcstats2table to extract all ROIs or a particular ROI for a group of
subjects.
doug
On 10/23/2014 09:00 AM, Smith, Michael wrote:
> I guess I'm not entirely sure how to do that? Are there any tutorials on how
> to extract
Hi Tracy,
if you mean how the method works internally:
the input image is registered to it's left right flipped version and
mapped into the midspace. this makes the image upright and straight (see
HBM abstract
*Robust and Accurate Contralateral Registration for Pose Normalization
and Tumor Se
Hello Claire,
Sorry this has been such a pain. There has been some reports that the
newer versions of XQuartz may have broken some of the freesurfer GUIs.
Could you please try deleting XQuartz again an resinstalling XQuartz
version 2.7.5. You can download it from this page:
http://xquartz.maco
Matt,
Can you send me the actual recon-all.log file? It might be helpful for
me to diagnose the issue. Thanks.
-Zeke
On 10/23/2014 07:48 AM, Matthew Riddle wrote:
> Dear Freesurfer Team,
>
> I recently installed Freesurfer on a new Macbook pro, which was upgraded
> to Yosemite, and I re-install
Dear group,
Is there a way to create a prefrontal cortex label in fresurfer? if so,
please tell me the exact steps to do so, I am very confused.
Thank you,
Anna
___
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Hi Michael
you can use mri_annotation2label to extract a specific label from the
aparc file and go from there.
cheers
Bruce
On Thu, 23 Oct 2014, Smith, Michael wrote:
> I guess I'm not entirely sure how to do that? Are there any tutorials on how
> to extract an ROI from the aparc.stats file?
>
I guess I'm not entirely sure how to do that? Are there any tutorials on how to
extract an ROI from the aparc.stats file?
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Wednesday, October
Dear Freesurfer Team,
I recently installed Freesurfer on a new Macbook pro, which was upgraded to
Yosemite, and I re-installed X11 after the upgrade, but I’m still experiencing
an issue with freesurfer that I’m hoping you might have some idea about.
Just to test the install and see what my tota
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Hello again Bruce,
Thanks so much for your reply. I tried uninstalling XQuartz completely and
reinstalling it, and I`m still getting the bus error. I have XQuartz`s
newest version (2.7.7) that was launched in August of this year installed
and it works with Macs 10.6 and newer.
My Mac environment i
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