Dear freesurfer experts:
I am trying to process an MRI using recon-all -autorecon1 -autorecon2
-autorecon3
and exited with errors. Apparently the encoded image data is not supported
(below you can see the recon-all.log)
Is there a way to process this study?
Thank you very much for your help
thanks very much doug.
cheers,
satra
On Tue, Oct 8, 2013 at 11:55 AM, Douglas N Greve
wrote:
>
> On 10/08/2013 09:17 AM, Satrajit Ghosh wrote:
> > hi folks,
> >
> > i'm using mri_vol2surf to map functional time series into
> > fsaverage3/4. my assumption is that each vertex time series will be
I see. Thank you so much for everything!
Tara
- Original Message -
From: "Douglas N Greve"
To: "Tara Ann Miskovich"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 8, 2013 2:42:36 PM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
it gives you est
it gives you estimates of whatever you give it. If the y.mgh file are
pial estimates, then that is what you will get
doug
On 10/08/2013 03:40 PM, Tara Ann Miskovich wrote:
> opps sorry one last question. Will segstats get me LGI estimates of the pial
> surface?
>
> Tara
>
> - Original Mess
opps sorry one last question. Will segstats get me LGI estimates of the pial
surface?
Tara
- Original Message -
From: "Douglas N Greve"
To: "Tara Ann Miskovich"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 8, 2013 2:15:33 PM
Subject: Re: [Freesurfer] Cluster Annotation fil
Thank you so much!
Tara
- Original Message -
From: "Douglas N Greve"
To: "Tara Ann Miskovich"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 8, 2013 2:15:33 PM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
OK, the feature that computes that fil
OK, the feature that computes that file was added after that. One thing
you can do is to download 5.3 and use 5.3 to do your stats. There should
not be any difference. Alternatively, you can run mri_segstats yourself,
something like
mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.ocn.mgh --avgw
version 5.0.0
- Original Message -
From: "Douglas N Greve"
To: "Tara Ann Miskovich"
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, October 8, 2013 1:57:35 PM
Subject: Re: [Freesurfer] Cluster Annotation file and mris_anatomical_stats
what version of FS are you using?
On 10/08/2013
what version of FS are you using?
On 10/08/2013 02:55 PM, Tara Ann Miskovich wrote:
> I did. This is what I get from my group analysis in the folder. I didn't find
> the ocn.dat file. Is there something I need to do in Qdec to produce it?
>
> C.dat maxvox.dat mc-z
I did. This is what I get from my group analysis in the folder. I didn't find
the ocn.dat file. Is there something I need to do in Qdec to produce it?
C.dat maxvox.dat mc-z.abs.th13.sig.ocn.mgh
cnr.mgh mc-z.abs.th13.pdf.dat mc-z.abs.th13.sig.vert
On 10/08/2013 09:17 AM, Satrajit Ghosh wrote:
> hi folks,
>
> i'm using mri_vol2surf to map functional time series into
> fsaverage3/4. my assumption is that each vertex time series will be
> the mean over an icosahedral patch corresponding to the vertex on
> fsaverage. is that how the resampli
Did you generate the annotation from a qdec analysis of lgi? If so, then
there should be a file already there called something like
mc-z.abs.th13.sig.ocn.dat with a row for each subject and a column for
each cluster. The value will be the mean lgi for that subject and
cluster. Is this what you
Can you send the aseg.stats file for subj1 and subj2?
On 10/08/2013 07:53 AM, Daniel Ferreira wrote:
> Dear Douglas,
>
> I generated my table with version 5.3.
>
> Attached is an example for two subjects (in .txt and .xls formats).
>
> Best regards
>
> Dani
>
>
>
>
Wow! That was fast.
I am running FreeSurfer 5.3 on top of CentOS6 (64-bit). My hardware is a
PC powered by Intel® Core™ i5 CPU M 520 @ 2.40GHz × 4
Thank you for all help.
Cheers
Marcos.
Em Ter, 2013-10-08 às 09:00 -0400, Bruce Fischl escreveu:
> Hi Marcos
>
> I've fixed this problem, which is a bu
Hi Ruth, use this version of mni152reg
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg
mri_label2vol can go in both directions (and can take any file types,
ie, mgz, nii, nii.gz, etc)
doug
On 10/08/2013 01:34 AM, Ruth Carper wrote:
> Hi Doug,
> mri_label2vol says it cre
Try now
On 10/07/2013 08:31 PM, EK Kim wrote:
> Dear experts,
> I updated FreeSurfer as a 5.3.0 version but have a problem about the
> missing ribbon.mgz when running recon-all procedure.
> I found the ftp address but couldn't find the mri_segstats.
> (ftp:/surfer.nmr.mgh.harvard.edu/transfer/ou
hi folks,
i'm using mri_vol2surf to map functional time series into fsaverage3/4. my
assumption is that each vertex time series will be the mean over an
icosahedral patch corresponding to the vertex on fsaverage. is that how the
resampling is done? also is the resampling done with a single interpo
I see, could you help me go about this. I have not been able to figure out how
to do this with an annotation file. And I believe I already mapped my lgi to
fsaverage space before group level through recon-all -qcache. Is this what you
mean?
Thank you again for the help!
Tara
- Original Me
Hi Marcos
I've fixed this problem, which is a bug in one of the open source math
libraries we use. If you email us the details of your hardware/software
environment we'll get you a patch.
cheers
Bruce
On Mon, 7 Oct 2013, Marcos Martins da
Silva wrote:
Hi, Bruce
I proceeded as explained at
Hi Olof
what are the dimensions of the volumes that fail? If you upload one we will
take a look. Is it a display problem or is the volume actually cropped? Try
looking at the .mgz in different viewers (freeview, fslview) and see if it
is still an issue
cheers
Bruce
On Tue, 8 Oct 2013, Erik
ok, I just downloaded it and am trying to replicate your problem now
On Tue,
8 Oct 2013, Marcos Martins da Silva wrote:
Hi, Bruce
Filedrop worked great and fast! Thank you for the tip.
It follows the bath I run for each subject:
mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippo lh.surfHippo
Dear Douglas,
I generated my table with version 5.3.
Attached is an example for two subjects (in .txt and .xls formats).
Best regards
Dani
Measure:volume Left-Lateral-Ventricle Left-Inf-Lat-Vent
Left-Cerebellum-White-MatterLeft-Cerebellum-Cortex Left-Thalamus-Proper
Left-Cauda
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