Hi MGH folks,
Update to previous report:
Review: Both of my attempts from scratch to CVS the 5.3.0 source failed after
about 760 files, directory trctrain. CVS quit with fatal signal 9 error.
Previously when I tried to restart either of these, CVS would quickly run
through all the up-to-date d
Hello Graham,
Thanks for the update. The read-only CVS server can be somewhat unstable
at times, but this looks like a new error I have not seen before. I am
looking into it now and will send an update when the issue is resolved.
-Zeke
On 05/31/2013 05:09 PM, Graham Wideman wrote:
> Hi MGH fol
thanks!
caspar
2013/5/31 Bruce Fischl :
> oh, my mistake. I thought it called them with specific parms. Sorry:
>
> for mri_segment:
>
> gray_hi = 99 ; (same as --ghi 99)
> wm_low = 89 ;(same as -wlo 89)
>
>
> for mri_normalize:
>
> intensity_below = 15 ; (same as -b 15)
>
> cheers
> Bruce
>
oh, my mistake. I thought it called them with specific parms. Sorry:
for mri_segment:
gray_hi = 99 ; (same as --ghi 99)
wm_low = 89 ;(same as -wlo 89)
for mri_normalize:
intensity_below = 15 ; (same as -b 15)
cheers
Bruce
On Fri,
31 May 2013, Caspar M. Schwiedrzik wrote:
yes, but
Hi MGH folks,
I am attempting to download the source via CVS as described here:
http://freesurfer.net/fswiki/ReadOnlyCVS
using:
cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P
-r release_5_3_0 dev
(ie: 5.3.0 source)
The CVS process is consistently stopping about
Oh, right, it is probably not there for subcortical. I don't know what I
would have to do to write it out. It won't be something that happens
before I get back from HBM. Can you remind me after HBM?
doug
On 05/31/2013 04:44 PM, Joseph Dien wrote:
> It looks like the corrected vertex p-values
>
It looks like the corrected vertex p-values (ex:
cache.th13.abs.sig.voxel.nii.gz) are only available for the surface-based lh
and rh spaces. For the subcortical volume-based analysis I don't see the
corresponding corrected voxel p-values being available?
On May 31, 2013, at 2:46 PM, Joseph Die
Hi Robert
I'm really sorry to hear it. I suspect that though that you would be better
off rerunning everything through 5.3. It should be the case that all manual
edits are retained and it's just compute time that you will have wasted.
5.2 had a user-requested mod that made the surfaces inaccur
mri_normalize is a binary so you can't, just recon-all.
On Fri, 31 May 2013, Caspar M. Schwiedrzik wrote:
I only find flags for mri_normalize and mri_segment in recon-all, and I have
trouble reading the contents mri_normalize with a regular text editor.
caspar
2013/5/31 Bruce Fischl
Hi
Sorry, I misinterpreted your question. In that case, if you want more than the broad-brush description that Bruce provided, you'll likely need to download the source code and scour the c-code yourself to find the exact specifics.
cheers,
-MH
--
Michael Harms, Ph.D.
--
yes, but recon-all just calls mri_segment with -mprage and mri_normalize
with -mprage.
I would like to know what -mprage does in these two functions, but i cannot
search them because they are executables, not scripts.
Caspar
2013/5/31 Harms, Michael
>
> Use any editor (even Word) with a search
you can just specify an overlay on the freeview command line
On 05/31/2013 03:26 PM, Salil Soman wrote:
> I have been able to generate the table. I was asking about an actual
> image (that could be visualized in freeview or something else).
>
> Thank you.
>
> -S
>
>
> On Fri, May 31, 2013 at 12:2
I have been able to generate the table. I was asking about an actual image
(that could be visualized in freeview or something else).
Thank you.
-S
On Fri, May 31, 2013 at 12:25 PM, Douglas N Greve wrote:
> Do you mean table data or data that you have on a map?
>
> On 05/31/2013 03:20 PM, Sali
Do you mean table data or data that you have on a map?
On 05/31/2013 03:20 PM, Salil Soman wrote:
> Dear Doug,
>
> Thank you for your recent advise with using freesurfer to extract mean
> values from non structural image data. Is there a way to generate an
> image (e.g. heat map) displaying those
On 05/31/2013 02:45 PM, Joseph Dien wrote:
>
> On May 31, 2013, at 12:09 PM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>>
>> On 05/30/2013 04:37 PM, Joseph Dien wrote:
>>> Just to make sure I'm doing this right, I'm going to summarize what
>>> I've taken away from your answers
Hi Bruce and others,
We started a rather extensive push of data through the linux 5.2 release of
free surfer. We also use OS X at times and I was hoping to get a R5.2 for MAC
but I see it's not available. One of the guys that works in my lab — Jon Holt —
also said that 5.2 was no longer availab
Dear Doug,
Thank you for your recent advise with using freesurfer to extract mean
values from non structural image data. Is there a way to generate an image
(e.g. heat map) displaying those values in free view?
Best wishes,
Sal
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Freesurfer mailing l
I only find flags for mri_normalize and mri_segment in recon-all, and I
have trouble reading the contents mri_normalize with a regular text editor.
caspar
2013/5/31 Bruce Fischl
> Hi Caspar
>
> it changes some parameters to the intensity normalization and segmentation
> to account for the lower
On May 31, 2013, at 12:11 PM, Douglas N Greve wrote:
>
> On 05/31/2013 01:49 AM, Joseph Dien wrote:
>> I was able to make more progress so I'm mostly good at this point but
>> I have a remaining question:
>>
>> I assume the contents of sig.nii.gz (which I assume are the vertex
>> p-values) a
On May 31, 2013, at 12:09 PM, Douglas N Greve wrote:
>
> On 05/30/2013 04:37 PM, Joseph Dien wrote:
>> Just to make sure I'm doing this right, I'm going to summarize what
>> I've taken away from your answers and to ask some new questions. In
>> order to present the results, I need two things:
the white surface uses information such as the surface normal and
surface-based smoothing to refine the estimate of the gray/white boundary,
so in general it is significantly more accurate. The orig is really just an
initialization for the white
cheers
Bruce
On Fri, 31 May 2013, Jonathan Holt
Always wondered, was never quite sure. I'm wondering why sometimes they
mirror each other and other times they shift away.
jon
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The i
Thank you!
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, May 31, 2013 1:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Group
mri_glmfit does not do it. Run mris_preproc. See the tutorial
doug
On 05/31/2013 01:13 PM, Fotiadis, Panagiotis wrote:
> Hey Doug,
>
> Is there any need to co-register the subjects (of the two cohorts) destined
> for group analysis to the fsaverage space first in order to be able to
> compare
Hey Doug,
Is there any need to co-register the subjects (of the two cohorts) destined for
group analysis to the fsaverage space first in order to be able to compare
their cortical thickness on the same space, or does mri_glmfit do that?
Thanks again,
Panos
__
Hi Douglas:
The file is the OAS1_0001_MR1 case of OASIS-BRAINS database that I
re-processed using freesurfer 5.2.0...
Sincerely,
Gonzalo Rojas Costa
On Fri, May 31, 2013 at 12:12 PM, Douglas N Greve
wrote:
> don't know what's going on. Can you upload the subject to our file drop?
> doug
>
Thanks!
Panos
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, May 31, 2013 12:22 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Gr
yes
doug
On 05/31/2013 12:16 PM, Fotiadis, Panagiotis wrote:
> Hey Doug,
>
> Great, but besides the unbalanced numbers in each cohort, the fact that we
> have a cross sectional analysis instead of a longitudinal one doesn't matter
> right? Would it be correct to say that we still apply the same g
Hey Doug,
Great, but besides the unbalanced numbers in each cohort, the fact that we have
a cross sectional analysis instead of a longitudinal one doesn't matter right?
Would it be correct to say that we still apply the same group analysis
described in the wiki?
Thanks,
Panos
_
There should be a file called something like cache.th13.abs.y.ocn.dat.
This will have a column for each cluster and a row for each subject. The
value in the row will be the input for each subject.
doug
On 05/30/2013 11:21 PM, Joshua deSouza wrote:
> Hello everyone,
>
> Please pardon my rather si
don't know what's going on. Can you upload the subject to our file drop?
doug
On 05/30/2013 04:36 PM, Gonzalo Rojas Costa wrote:
> Hi Doug:
>
>The command is:
>
> mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown
> --volmask --o mri/lobulitos.mgz --annot lobulos --wmparc-d
On 05/31/2013 01:49 AM, Joseph Dien wrote:
> I was able to make more progress so I'm mostly good at this point but
> I have a remaining question:
>
> I assume the contents of sig.nii.gz (which I assume are the vertex
> p-values) are not FWE corrected. Is it possible to get FWE-corrected
> vert
On 05/30/2013 04:37 PM, Joseph Dien wrote:
> Just to make sure I'm doing this right, I'm going to summarize what
> I've taken away from your answers and to ask some new questions. In
> order to present the results, I need two things:
>
> 1) A set of histograms (with error bars) for each cluster
Hi Bruce and Thomas,
Thanks so much for your help! I think I have a better idea now.
Best,
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 5/31/13 11:23 AM, "Bruce Fischl"
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi Danie
Hi Panos, are you asking whether theunbalanced design will leadto one
slope being different than another just because the numbers are
different? That is not a problem. You can simply follow the instructions
on the wiki.
doug
On 05/31/2013 11:26 AM, Fotiadis, Panagiotis wrote:
> Hey Doug,
>
>
Thanks! it is working perfectly, I created a command file to take several
screenshots, for example:
[...]
-cam azimuth 90
-ss imagen6.png
-cam azimuth 90
-cam Elevation 90
-ss imagen7.png
-slice 127 180 127
-ss imagen8.png
-slice 127 80 127
-cam Elevation 180
-ss imagen9.png
-quit
On Fri, May 3
If you use '-ss' option, freeview will save a screenshot and close
itself. For example:
freeview -v foo.mgz -ss foo.jpg
On 05/31/2013 11:13 AM, Ender Konukoglu wrote:
Sure.
I couldn't find that option neither.
What I did was to semi-automatize.
I wrote a batch file to call freeview multiple
Hey Doug,
Sorry for the overwhelming amount of questions. I wanted to confirm something.
Suppose you want to do group analysis between two groups say a healthy cohort
vs a diseased cohort. Each cohort has ~40 and ~30 subjects each (different
people), and you want to compare how for instance the
Hi Daniel
it's a bunch of things like substancia nigra, the subthalamic nucleus,
LGN (I think), etc
Bruce
On Fri, 31 May 2013, Yang, Daniel wrote:
Dear all,
in the aseg.volume, there is a term called 'ventral DC' and I am wondering
what it is.
I looked up the previous posts and know DC
Thanks Ender,
I am trying to make a command file with multiple commands too in order to
have snapshots from different views.
thanks for the help!
Gari
On Fri, May 31, 2013 at 5:13 PM, Ender Konukoglu wrote:
> Sure.
>
> I couldn't find that option neither.
>
> What I did was to semi-automatize
Hi Jon
the parcellation labels are usually pretty accurate, particularly since
gyral borders are pretty arbitrary. I wouldn't touch them unless you see a
dramatic and obvious failure (e.g. precentral gyrus labeled as
post-central). This happens pretty rarely though
Bruce
On Fri, 31 May
2013,
Sure.
I couldn't find that option neither.
What I did was to semi-automatize.
I wrote a batch file to call freeview multiple times with different
parameters.
Each time freeview pops up and I save the image/video. During this time
the process in the terminal waits for me.
When I shut that wind
Hi all,
We are using the parcellation of Desikan-Killiany
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
and creating labels for each structure in each hemisphere with:
mri_annotation2label --subject ${SUBJ} --hemi ${HEMI} --outdir
${SUBJ}/${SUBJ}_annotate
and making matlab tex
Thanks!
I can visualize the 3D renders of interest with different colors, but from
"freeview -h" I couldn't get the following: is it possible to automatize
the "File > Save movie frames" option?
Thanks again!
Gari
On Fri, May 31, 2013 at 4:59 PM, Juan Eugenio Iglesias <
igles...@nmr.mgh.harvar
Ender asked me to forward you this:
I had to automate freeview recently.
Freeview can be used via command line.
For options please write
freeview -h
in the console / terminal.
An example command that produces a surface and overlays a map on it:
freeview -f lh.inflated:overlay=L.mgz -cam azimuth 1
Dear all,
in the aseg.volume, there is a term called 'ventral DC' and I am wondering what
it is.
I looked up the previous posts and know DC = diencephalon, and it's a grab bag
of stuff that cannot be resolved.
However, does anyone know what exactly ventral DC is?
Thanks!
Daniel
--
Yung-Jui "
Yes, in each analysis directory there is a meanfunc.nii.
Maybe this summer I will switch to FS5, but I have a bunch of experiments
in 4.5 and am not 100% comfortable with the way the retinotopy analysis
needs to be done in FS5, which is a vital component of my work.
Katie
On Thu, May 30, 2013 a
Anna, if you need to get it back into the native anatomical space, see
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
You can use nii as the output format instead of mgz
doug
On 5/31/13 7:23 AM, Anna Josefson wrote:
Dear FreeSurfer users!
I am new to Freesurfer, and I have s
Hi Sudhin
have you looked at the defect to see what is causing it? It's very big,
which is probably the root of the problem.
Bruce
On Fri, 31 May 2013, Sudhin A.
Shah wrote:
On May 28, 2013, at 3:48 PM, Sudhin A. Shah wrote:
CORRECTING DEFECT 1 (vertices=33, convex hull=57)
A
On May 28, 2013, at 3:48 PM, Sudhin A. Shah wrote:
CORRECTING DEFECT 1 (vertices=33, convex hull=57)
After retessellation of defect 1, euler #=-41 (88676,260208,171491) :
difference with theory (-61) = -20
CORRECTING DEFECT 2 (vertices=30163, convex hull=6211)
error in the retessellation
normal
Hi Cris
it really depends on your data quality. If it's good then you might be
fine most of the time. You should scroll through the slices in tkmedit with
the surfaces overlaid to verify that they do indeed follow the gray/white
and pial boundaries.
cheers
Bruce
On Fri, 31 May 2013, Cristian
Hi Caspar
it changes some parameters to the intensity normalization and segmentation
to account for the lower SNR and increased CNR in the mprage. You'll need
to look in the recon-all script for the details
cheers
Bruce
On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote:
Hi!
Is there more d
Great, thank you for your help!
Panos
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, May 30, 2013 5:39 PM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons error
you
Thanks a lot Anastasia.
I had an extra volume at the end of file which was just an average of all other
volumes (automatically generated by philips scanner). Removing that extra
volume solved my problem.
Thank you again,
Ali Ezzati
From: Anastasia Yendik
There is a screenshot option -ss from the command-line. Run 'freeview -h' will
show you all the available options.
Ruopeng
On May 31, 2013, at 6:16 AM, Garikoitz Lerma-Usabiaga
wrote:
> Hi list,
> is it possible to automate Freeview automation from the command line?
>
> I want to automati
Hello FS-ers,
I have a beginner question.
I am wondering about editing. Since I have no superior of me in my lab to
inspect or guide me in my freesurfer analyses - I get a bit worried that I
might oversee some important errors from recon-all.
If there is nothing that is strikingly wrong in the
use mri_convertcheck this
linkhttps://surfer.nmr.mgh.harvard.edu/pub/docs/html/mri_convert.help.xml.html
Azeez Adebimpe
Date: Fri, 31 May 2013 13:23:20 +0200
From: anna.b.josef...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Conversion
Dear FreeSurfer users!
I am new to
Dear FreeSurfer users!
I am new to Freesurfer, and I have succesfully managed to run recon-all on
my data, for every subject.
Now I plan to use the output - some of the different cortical and
subcortical brain structures as ROI's in my SPM analyses.
Then I would have to convert from freesurfer
Hi list,
is it possible to automate Freeview automation from the command line?
I want to automatically render 3D images of the hippocampus (I have a
separate volume, based on hippo-subfields) and have an image for all
subjects for quality checking.
thanks!
Gari
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