Dear freesurfers,
Which stimuli do you think provide the best retinotopic maps?
I have done a retinotopy analysis using the following stimuli:
Polar angle:
- 45 deg counter-clockwise rotating wedge
- 8 unique positions
- flickering at 2 Hz
- stimulation period: 36 sec
- no. of cycles: 6
- TR
Hi Nick,
I have Mac OS X 10.6.7.
Now I found the tmp folder, and can explain in more details what happens:
As I save the Project File, the qdec_project_archive/qdec.table.dat is
created, but it exists in /tmp only for several seconds and then
disappears.
Have you heard about something like this
Dear Freesurfers,
I was wondering if you could help me clarify one question I have re
the recommended use of bbregister to register PET data.
If I want to register my PET data to MNI305 space used in Freesurfer,
is a 6 dof rigid registration enough?
I notice that the tailarach function used
Hi Joao
You are registering to that subject's anatomicals, not a template, so 6 should
be enough
Cheers
Bruce
On Jul 7, 2011, at 6:43 AM, Joao Pereira jm...@wbic.cam.ac.uk wrote:
Joao
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Hi freesurfers
Do anyone know if it's possible to automatically enter in the QDEC table the
gray matter volume of every subject in the study, to avoid
entering this item manually for each one ?
Best regards.
--
Ignacio.
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Hi guys,
I've got a list of fiducials (fcsv) from 3DSlicer, Is there a way to
import them within freeview? Those points look like
label,x,y,z,[flag],[flag]
i.e.
P,57.799,-49.1799,13.07,1,1
P,-4.05607,-47.1519,8.93645,1,1
thank in advance.
g.
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Hi Jorge,
Thanks for your reply, I installed Octave in the Ubuntu machine, Should I
setup something in order to use the FS commands?
Best regards,
Carolina
2011/7/5 jorge luis jbernal0...@yahoo.es
Hi Carolina
**
There is a directory freesurfer/matlab which contains several
Hello FSexperts
I have a MPRAGE image of cortical dysplasia, I have some regions of
grey matter within the white matter, and I measured the cortical
thickness in the projections of those regions and I expected to find a
thinnercortex instead I found a cortical thickening. FS takes into
account
Carolina,
We have worked with several cases of MCD (including cortical dysplasia). We
have published this paper:
https://surfer.nmr.mgh.harvard.edu/pub/articles/jon_372_LR.pdf
It may help.
But in most cases of cortical dysplasia (not Gray matter heterotopia cases)
you'll find a ticker cortex
The conversion from PET to MNI305 uses two registration steps. One from
PET to anatomical, one from anat to mni305. bbregister handles the first
one, so 6 dof is fine.
doug
Joao Pereira wrote:
Dear Freesurfers,
I was wondering if you could help me clarify one question I have re
the
Hi Paola, I can't tell from the output what went wrong. One thing that
may be going wrong is that you might not have the matlab binary in your
path. From a terminal, type 'which matlab' (no quotes). Also, please
don't send logs and error messages in rtf or doc formats -- it makes it
harder for
Dear all,
I created a 3-frame image using a command similar to:
mris_preproc --target fsaverage --hemi lh --fwhm 5 \
--out xrun/lh.cope1.mgh \
--iv fbert1.feat/stats/cope1.nii.gz
fbert1.feat/reg/freesurfer/anat2exf.register.dat \
--iv fbert2.feat/stats/cope1.nii.gz
Hi Aga, try View-Configure-Overlay. The config window will have a time
point entry at the top.
doug
Agnieszka Burzynska wrote:
Dear all,
I created a 3-frame image using a command similar to:
mris_preproc --target fsaverage --hemi lh --fwhm 5 \
--out xrun/lh.cope1.mgh \
--iv
Hi all
Could anyone help me with this error:
MRISreadAnnotationIntoArray: vertex index out of range: 1499028058
i=5A595959, in_array_size=133467
annot file:
/home/virtualuser/apps/freesurfer/subjects/s1/surf/../label/lh.aparc.annot
This appeared after trying to average my subject data. It says
Dear Doug,
Yes, it works, thank you so much!
Cheers,
Aga
On 7/7/11 3:57 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
Hi Aga, try View-Configure-Overlay. The config window will have a time
point entry at the top.
doug
Agnieszka Burzynska wrote:
Dear all,
I created a 3-frame image
Hi Leo, check to see if that subject's analysis is up-to-date. This
usually happens when it was only partially re-run.
doug
leonardo kay wrote:
Hi all
Could anyone help me with this error:
MRISreadAnnotationIntoArray: vertex index out of range: 1499028058
i=5A595959, in_array_size=133467
Hi Michelle, do the eccen and polar maps look ok? Also, I would probably
smooth them a little bit. The field sign calculation is basically a
spatial derivative so it can be sensitive to noise.
doug
Michelle Umali wrote:
Dear all,
I've been having issues with my fieldsign images all I
the 'generate stats data tables' button in the Subjects tab will do
this. see the section 'Stats Data Import' in the tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis
which is copied here:
It is possible to import the aseg and aparc data from the
Dear all,
I am combining 3 runs of a subject using fixed effects GLM and I wanted to
make sure I am doing the right thing.
For each subject I use:
mri_glmfit --y 3runs/lh.cope1.mgh --yffxvar 3runs/lh.varcope1.mgh --ffxdof
126 --osgm --glmdir 3runs/lh.osgm.ffx --surf fsaverage lh --label
Hi Aga, your commands look right. For the DOF, it should be the sum of
the DOFs from all the runs (probably won't make much of a difference).
Smoothing is a bit of an issue when you want to look at individual
results. Technically, you should smooth before you do the first level
analysis (ie,
Dear Doug,
Thank you so much. I completely see you point, but I have re-run the 1st
level feat without smoothing just because it has been recommended not to
smooth in the volume and then transfer it onto the surface, but rather first
smooth on the surface
I'd also be very interested to hear about good reinotopic stimuli; we've
used 6Hz and 14 ring sizes for eccentricity mapping in the past.
Thomas Ballinger
On Thu, Jul 7, 2011 at 3:56 AM, Anders Hougaard ahouga...@dadlnet.dkwrote:
Dear freesurfers,
Which stimuli do you think provide the best
The problem with doing the smoothing at the first level in FEAT is that
it will be volume-based, not surface-based. I'm not sure what to tell
you about using the varcopes. They will certainly be very noisy without
smoothing, so probably smoothing is a good idea, even if it's volume-based.
doug
Great, good to know. My LANG is en_US.UTF-8, everything else is not set.
On Thu, 7 Jul 2011, Franz Liem wrote:
Dear Anastasia all.
I fixed it.
The problem was my LOCALE setting which leads to different handling of
decimal separators by awk (for further details see
hi anders,
the optimal set of stimulus parameters will depend somewhat on what
cortical area(s) you are trying to map and on the details of your
acquisition. in general, stimulating with both clockwise- and
counterclockwise-rotating wedges for polar angle mapping and with both
expanding and
Hi Anders,
I agree with the points Jon made. 8 Hz flicker is also what I use. I haven't
tried lower frequencies, but
I think you would definitely have reduced SNR if you did. I also use rather
thin wedges and rings and smoothly vary their position.
I would add that a longer cycle
Hi FSexperts,
I have a case of a child with *Hydrocephalus and cortical dysplasia, the
patient has a subcutaneous ventriculo-peritoneal shunt that produces an
artifice in all MRI sequences, I try to recon-all but it exit with ERROR*
#
#@# Talairach
Hi Carolina
You simply need to add the path ‘your FS installation dir/freesurfer/matlab’
to the search path in Octave:
addpath(‘your FS installation dir/freesurfer/matlab’);
For example, to build a histogram of cortical thickness values for the first
subject of your study, you can try:
Yep, use
tkregister2 --s subject --fstal
there are instructions in the trouble shooting tutorial on the wiki.
doug
Carolina Valencia wrote:
Hi FSexperts,
I have a case of a child with /Hydrocephalus and cortical dysplasia,
the patient has a subcutaneous ventriculo-peritoneal shunt that
Hi Antonella,
did bert inflated look ok on the other computer? Usually this problem
goes away if you update the video card driver.
cheers
Bruce
On Thu, 7 Jul 2011, Antonella
Kis wrote:
Good afternoon Bruce,
I am still trying to fix my error related to the surface image display when
Best,
Chindhuri Selvadurai
Psychiatric Neuroimaging, Manoach Lab
Martinos Center for Biomedical Imaging, MGH
Phone: (617)726-0307
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Hi Doug,
The eccen and polar maps look ok, although activation tends to be
limited to the occipital poles and lateral surface not really along
the calcarine.
Is it possible to find out how the colors in the eccen and polar
images correspond to positions in the stimulus using rtview?
I am getting an error when using a script that combines these 3 actions:
preproc.sh
std_map_qc_montages.bash
put_tpef.bash
Freesurfer version 4
SUBJECTS_DIR: /cluster/manoach/AS/RespMon12C/subjects
Script:
/cluster/manoach/AS/RespMon12C/scripts/preproc_std_qc_montages_put_tpef.sh
It looks like
are you sure it's registered well to the anatomical/surface?
On Thu, 7 Jul
2011, Michelle Umali wrote:
Hi Doug,
The eccen and polar maps look ok, although activation tends to be
limited to the occipital poles and lateral surface not really along
the calcarine.
Is it possible to find out
Hi,freesurfers:
Recently,I read a paper which used freesurfer to processed their data,this
is the paper's
link:http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0060159
In this paper,the antor said :
One of the critical steps of the whole procedure was to partition the
Hi,
I am using Tracula, a new tool that comes with version 5.1.0 of FreeSurfer.
However, my data set are processed with the recon-all of an earlier version of
FreeSurfer: 5.0.0. I wonder whether I need to rerun recon-all on all the
subjects in the data set with 5.1.0. Would running Tracula on
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