Hi Martin,
Many thanks for your reply!
I did follow all the steps as described in the wiki.
I'm not sure i understand your suggestion though..
Are you proposing that, instead of using the cross.qdec.table, i should use
the longitudinal table to see the difference between two time points?
My lo
Dear Freesurfers,
I am working on a retinotopy analysis and I got this error:
ERROR: dimension mismatch between mask and surf when trying to look at
map angle in tksurfer-sess
Do I need to add --reshape flag? If so, where?
Any help would be most appreciated.
Thanks.
Michelle
Here are the analysi
Dear FS team,
I'm working on some NIFTI images which I want to convert to mgz. When I try
to do this, I get:
mri_convert
/home/avdleij1/ID1000/ID1000_scans/CON_ID1000/NIFTI/sc0219-20101101-0003-T13DTFESENSE.nii.gz
/home/avdleij1/ID1000/ID1000_scans/CON_ID1000/FREESURFER/mri/orig/001.mgz
$Id: mri_
try running mri_convert directly on the dicom
cheers
Bruce
On Tue, 27 Sep 2011, Andries R. Van
Der Leij wrote:
Dear FS team,
I'm working on some NIFTI images which I want to convert to mgz. When I try
to do this, I get:
mri_convert/home/avdleij1/ID1000/ID1000_scans/CON_ID1000/NIFTI/sc0219
LinkedIn
Mohan Boddu souhaite se connecter à vous sur LinkedIn :
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Freesurfer,
Je vous invite à faire partie de mon réseau professionnel en ligne sur le site
LinkedIn.
Accepter l'invitation de Mohan Boddu
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LinkedIn
Mohan Boddu souhaite se connecter à vous sur LinkedIn :
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Freesurfer,
Je vous invite à faire partie de mon réseau professionnel en ligne sur le site
LinkedIn.
Accepter l'invitation de Mohan Boddu
http://www.linkedin.com/e
Good morning Doug,
I will really appreciate if you can give me an advise on how I can get the mean
average of the cortical thickness value for the FDR clusters so before Monte
Carlo Simulation.
Many thanks,
Antonella___
Freesurfer mailing list
Freesu
Hi Joana,
no, what you did is fine. I just wanted to make sure that you are using
the cross table created from the long table (so that there is only a
single entry for each subject). It looks like that is the case.
Best, Martin
On Tue, 2011-09-27 at 12:11 +0200, Joana Braga Pereira wrote:
> Hi M
Dear Free Surfer,
I have gotten to 3. Configure Contrasts in
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastFirstLevel
When I run *mkcontrast-sess -analysis my-workmem.sm05.lh -contrast
encode-v-base -a 1*
I get the following result and error:
vermisii:fsfast-functional carla
Try giving it a -c 0
doug
Carl Anderson wrote:
> Dear Free Surfer,
>
> I have gotten to 3. Configure Contrasts
> in
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastFirstLevel
>
>
> When I run *mkcontrast-sess -analysis my-workmem.sm05.lh -contrast
> encode-v-base -a 1*
> I
Hi Michelle, did you change the structural after you ran the retinotopy
analysis? It looks like the number of vertices changed. If so, then
you'll need to re-run the fMRI analysis.
doug
Michelle Umali wrote:
> Dear Freesurfers,
> I am working on a retinotopy analysis and I got this error:
> ERRO
Why not run mri_glmfit-sim? It will give you the file that you want, and
it will be easier than me explaining all the stuff you'd need to do to
get it otherwise.
doug
Antonella Kis wrote:
> Good morning Doug,
>
>
> I will really appreciate if you can give me an advise on how I can get
> the mea
Run recon-all only with "-s subject -parcstats". This will regenerate
the ?h.aparc.stats file
doug
Keefe, Helen L wrote:
> Hi Everyone,
>
> I have not received a response on this question from August -= cold we
> revisit it please?
>
> thanks,
> Helen
>
>
> [Freesurfer] Saving annotation and s
HI Doug
Do we now have the means for computing point to point asymmetry differences
between RH and LH? I remember you mentioned we may have something on this line
with 5.1
Cheers
Lena
___
Lena Palaniyappan
Clinical Lecturer & Wellcome Trai
If you have two groups and you want to test for the differences in the
groups after you account for age, you need to do this in two steps.
First, set up a DODS model (ie, each group gets an intercept and a
slope). Use this to test for a difference between the slopes of the
groups ([0 0 1 -1]).
You can't just go and regress out age. You first have to make sure that
there is not an interaction between your age and group. That is done
with the first step that I described using the DODS model. Both of the
contrasts that you have below are for DODS, but you would only use the
2nd one. I k
Hi Doug,
I didn't change the structural after the analysis.
Before the retinotopy analysis, I ran recon-all -all, made some brainmask
and white matter edits, them ran autorecon2-wm and autorecon3. Finally, I
made occipital patches, then flattened them with mris_flatten.
When I ran this all before
Hello Freesurfer's,
I posted this last week. Does someone have any insights? Kindly advise!
Manish
-- Forwarded Message
From: , Manish Dalwani
Date: Fri, 23 Sep 2011 14:25:42 -0600
To:
Conversation: QDEC analyses
Subject: QDEC analyses
Hello Freesurfer's
I want to set up (thanks to Nick'
the easiest option is to download v5.1 and use the qdec in it. it will
include the necessary libs that qdec is built against.
n.
On Tue, 2011-09-27 at 11:13 -0600, Dalwani, Manish wrote:
> Hello Freesurfer’s,
>
> I posted this last week. Does someone have any insights? Kindly
> advise!
>
> Man
Thanks Nick, would that affect any of the files (or work) we have done on
Freesurfer version 4.5? Is there a way to use both seperately on the same
machine?
Best,
Manish
On 9/27/11 12:18 PM, "Nick Schmansky" wrote:
the easiest option is to download v5.1 and use the qdec in it. it will
inclu
its possible to have different versions installed, just install it in
another directory.
qdec will not change any of the existing data processed with another
version.
n.
On Tue, 2011-09-27 at 14:05 -0600, Dalwani, Manish wrote:
> Thanks Nick, would that affect any of the files (or work) we ha
Ok thanks so much Nick!
On 9/27/11 2:08 PM, "Nick Schmansky" wrote:
its possible to have different versions installed, just install it in
another directory.
qdec will not change any of the existing data processed with another
version.
n.
On Tue, 2011-09-27 at 14:05 -0600, Dalwani, Manish w
Hi,
I have a bunch of scans from patients with mulitple sclerosis. Since
they all have substantial t2w hyperintensities I would like to
automate the process of WM filling and re-running. Looking through the
emails and the wiki, however, I am a bit confused.
http://www.freesurfer.net/fswiki/FsTutor
Dear All,
I am trying to correlate clinical disability measure ALSFRS score with cortical
thickness in ALS patients. Attached is the fsgd file. I am not able to run
mris_preproc with this fsgd file "ERROR message: is no subjects specified"
what am I doing wrong here , also my design matrix con
Hi Doug,
this script resulted in the same problem - recon-all -all didn't run. It
was complaining that there is no 001.mgz. So we created 001.mgz with
recon-all using the RAS orientation flag, and popped it in the orig folder.
Then the recon ran through w/o errors, but all the fixes were gone (e.
Hi Doug and Freesurfers
I didn't change any of the structural After the retinotopy analysis.
First, I ran recon-all -all.
Second, I made edits to to brainmask.mgz and wm.mgz and then ran
autorecon2-wm and autorecon3.
Third, I cut the occipital patches in tksurfer and then flattened them.
Finally,
Dear Freesurfers,
This is related to my retinotopy analysis tksurfer-sess dimension
mismatch error message.
So another subject had these errors come up during fieldsign-sess
selxavg3-sess -a rtopy.self.lh -s sjXX -force
(which ran without error)
then I ran fieldsign
fieldsign-sess -a rtopy.self.l
hi,
we are seeing a strange freeview issue at mit and just wanted to check if
anybody else has seen this. we are running natty narwhal (ubuntu 11.04).
details here:
https://github.com/gablab/mindhive/issues/1
cheers,
satra
___
Freesurfer mailing list
The control points won't be copied over because they will be wrong
(though you can try changing the sign of the first coordinate). I'm
surprised that the skull strip edits were lost. Were they edits from the
brainmask.final surfs? I've put a new version of xhemireg in the same
place as before.
Is the occip patch out of synch with the subject? Does it run if you use
-sphere instead of -occip?
doug
Michelle Umali wrote:
> Dear Freesurfers,
> This is related to my retinotopy analysis tksurfer-sess dimension
> mismatch error message.
>
> So another subject had these errors come up during f
If you run 'glxgears' command, does it get similar error?
Ruopeng
On 9/27/11 8:40 PM, Satrajit Ghosh wrote:
hi,
we are seeing a strange freeview issue at mit and just wanted to check
if anybody else has seen this. we are running natty narwhal (ubuntu
11.04).
details here:
https://github.c
Hi Doug,
I get the same MRISripZeros() and MRIScopyMRI Surf/src mismatch error
when I use -sphere and not -occip in fieldsign-sess.
What else should I try?
Thank you.
Michelle
On Tue, Sep 27, 2011 at 8:51 PM, Douglas N Greve
wrote:
> Is the occip patch out of synch with the subject? Does it ru
Hi Freesurfers,
I want to do a PPI in FSL FEAT using the V1 left and righ found
generated in recon-all as seeds using:
I know for each subject I have to get a timecourse for my seeds
fslmeants -i filtered_func.nii.gz -o my_timecourse.txt -m V1_mask.nii.gz
For each subject, I've run reg-feat2anat
Dear Freesurfers,
could you please give me detailed information about the Bonferroni or
clusterwise correction we can do in Freesurfer? How much iterations? Is that
cluster- oder voxelwise? Is there anywhere a detailed description about the
correction options?
Best regards,
Viola
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