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I should have mentioned that the HCP data have been processed using
FS5.3HCP. If we know which code/script generates sulc files, we can try to
dig out the code to find the scaling factor.
On Thu, Nov 12, 2020 at 9:46 PM Reza Rajimehr wrote:
> Tha
Reza Rajimehr wrote:
> Hi,
>
> In the .sulc files, the range of sulcal depth values are very different
> (about 10 times higher) in Freesurfer v6 compared to Freesurfer v5.3. Is
> there just a simple scaling factor here, or the procedure for calculating
> sulcal depth has been c
External Email - Use Caution
Hi,
In the .sulc files, the range of sulcal depth values are very different
(about 10 times higher) in Freesurfer v6 compared to Freesurfer v5.3. Is
there just a simple scaling factor here, or the procedure for calculating
sulcal depth has been changed
You were right Bruce! mri_surf2surf worked for the curvature file. We
needed to specify --src_type and --trg_type as curv.
Best,
Reza
On Mon, Jun 12, 2017 at 12:52 PM Reza Rajimehr wrote:
> Thanks Bruce!
>
> mri_surf2surf does not accept a curvature file as an input. So we are
>
sulc on the surface (as
opposed to changing the way that the inflation works)
On Sun, Jun 11, 2017 at 11:52 PM Reza Rajimehr wrote:
> Hi,
>
> We have used mris_inflate:
>
> mris_inflate rh.smoothwm rh.inflated
>
> The command generates inflated and sulc files. We would like to
Hi,
We have used mris_inflate:
mris_inflate rh.smoothwm rh.inflated
The command generates inflated and sulc files. We would like to do a little
bit of smoothing on the sulc file, so that we get rid of few scattered
regions where small positive curvature islands are located within negative
curvat
04:02 PM, Reza Rajimehr wrote:
>* Hi Doug,
*>>* Since our external regressors are stimulus-related (e.g. mean
*>* luminance of stimuli), we need to convolve them with a hemodynamic
*>* response function. In mkanalysis-sess, we have used -spmhrf 0 to model
*>* conditions. Is there
exactly the
same spmhrf function for modeling the external regressors?
Thanks,
Reza
No, they are not
On 02/17/2017 05:09 PM, Reza Rajimehr wrote:
>* During the functional analysis in FS-FAST, are the external regressors
*>* convolved with the hemodynamic response function?
*>>* Than
During the functional analysis in FS-FAST, are the external regressors
convolved with the hemodynamic response function?
Thanks,
Reza
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In a functional analysis, we have a set of external regressors (e.g. mean
luminance of stimuli, size of stimuli, etc.). Should we normalize values
before including them in the regressor files? If so, what is the
recommended way of normalization ... z-scoring?
Thanks,
Reza
_
Hi,
In Tksurfer, we want to show functional activity map and borders of aparc
on a surface. The borders of aparc are always drawn on top of the activity
map, which sometimes hide small activation blobs. Is it possible to draw
the activity map on top of the aparc borders?
Reza
Hi,
Freesurfer has an annotation file for Brodmann areas, which is
?h.PALS_B12_Brodmann.annot. This Brodmann parcellation doesn't seem to be
accurate in certain regions (e.g. in retrosplenial and perirhinal cortex).
Does anyone have an alternative Brodmann atlas that can be visualized in
Freesurfe
). Then smooth by a certain FWHM (mri_surf2surf or mris_fwhm). This
will create a circle. If you divide all vertices by the value of the
vertex after smoothing and then threshold at 0.5, then you should have a
circle of radius approximately FWHM/2.
On Sunday, November 8, 2015, Reza Rajimehr wrote
Hi,
I want to draw a circle around a vertex on the smoothwm or pial surface,
with a particular radius (e.g. 10 mm), fill the circular region and save it
as a label file, then repeat this for all the vertices on the surface. I
need this for doing a searchlight analysis. Does anyone have a script/co
Hi,
We have run recon-all twice on a single subject, both times without any
error. Using a functional localizer, we have made a surface-based label for
an ROI (FFA) in the ventral temporal cortex of the inflated surface from
the first recon. When we visualize the same label on the inflated surface
Hi,
I have two questions:
1) In an fMRI experiment, we have 64 stimulus conditions and a baseline
condition. All conditions are presented in each run. After running the
analysis:
mkanalysis-sess -a category.rh -surface self rh -fsd bold -fwhm 3
-event-related -paradigm paradigm_category.par -nco
inux distro that people post to the list about in order to attempt
> replicate. But I'll install Ubuntu 14 on a laptop after OHBM concludes and
> investigate.
>
>
> -Zeke
>
>
>
> On Friday, June 12, 2015, Reza Rajimehr > wrote:
>
>> Hi Bruce,
>>
&g
-sess) and
seeing if they run. There might be some incompatibilities with freeview 5.3
doug
On Friday, June 12, 2015, Reza Rajimehr wrote:
> Hi Bruce,
>
>
> I guess I will eventually move to freeview - though I am not quite sure if it
> is easy to use with FS-FAST.
>
>
ry Linux distro that people post to the list about in order to attempt
replicate. But I'll install Ubuntu 14 on a laptop after OHBM concludes and
investigate.
-Zeke
On Friday, June 12, 2015, Reza Rajimehr wrote:
> Hi Bruce,
>
>
> I guess I will eventually move to freeview - t
resolved.
Best,
Reza
Hi Reza
can you use freeview for what you want instead? tksurfer and tkmedit are
deprecated
cheers
Bruce
On Thursday, June 11, 2015, Reza Rajimehr wrote:
> Hi,
>
> Is there any plan by the Freesurfer team to address this well-known bug?
>
> http://www.m
Hi,
Is there any plan by the Freesurfer team to address this well-known bug?
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35938.html
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36193.html
For now the only workaround is to enter values through command-line.
Thanks Doug! Could you clarify a bit more on how to "add up the dofs
in each run"?
You can mri_concat the cesvar files. For the dof, just add up the dofs
in each run.
On Monday, April 27, 2015, Reza Rajimehr wrote:
> If I use mri_concat instead of isxconcat-sess, will I
/outgoing/flat/greve/isxconcat-sess
If you just want to concatenate the vertex values, then just do
something like
mri_concat --o output.nii.gz sess1/bold/analysis/contrast/ces.nii.gz
sess2/bold/analysis/contrast/ces.nii.gz ...
On Monday, April 27, 2015, Reza Rajimehr wrote:
> Thanks D
Monday, April 27, 2015, Reza Rajimehr wrote:
> Hi,
>
> I am trying to use isxconcat-sess for averaging functional data across two
> monkeys. The data in two monkeys have been analyzed on a common surface
> (F99). When I run this:
>
> isxconcat-sess -sf MonkeysList.txt -analysi
Hi,
I am trying to use isxconcat-sess for averaging functional data across two
monkeys. The data in two monkeys have been analyzed on a common surface
(F99). When I run this:
isxconcat-sess -sf MonkeysList.txt -analysis movie2.task.rh -all-contrasts
-o group2
I get an error:
ERROR: cannot find
Hi,
In an fMRI experiment, I have 60 conditions. I want to make ALLvsFIX
contrast to select vertices that are visually responsive, by finding
vertices that have ces values greater than zero in this contrast. For
this, I can run:
mkcontrast-sess -analysis analysisname -contrast allvsfix -a 1 -a 2
10/09/2014 12:12 AM, Reza Rajimehr wrote:
> Hi Doug,
>
> Removing -i fmc did not help, and I still get the same error.
>
> By looking at the rawfunc2surf-sess script, it looks like specifying an
> argument for -surfreg makes ExpKeyNeeded = 1. Can I just specify something
> for -ex
?
Thanks,
Reza
Try it without -i fmc
On 10/08/2014 04:38 AM, Reza Rajimehr wrote:
> One more question:
>
> I tried to run:
>
> rawfunc2surf-sess -s oz_fparc -i fmc -trgsubject F99 -surfreg
> iter05.sphere.reg -fwhm 2 -per-session
>
> And I got this:
>
> ERROR: expert
One more question:
I tried to run:
rawfunc2surf-sess -s oz_fparc -i fmc -trgsubject F99 -surfreg
iter05.sphere.reg -fwhm 2 -per-session
And I got this:
ERROR: experts key needed (-expkey)
Not sure what this flag is.
Reza
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Hi,
I want to use rawfunc2surf-sess to project the functional data onto the
surface in the source subject and then in the target subject. My source
subject has been processed in Freesurfer. However, my target subject has
been processed in Caret, so I do not have all the surface files for the
targe
Hi Doug,
Before I saw your response, I modified make_average_surface code by
removing -annot aparc flag in the mris_make_template command within this
code, and my script worked fine all the way to the end without any error.
The change you made in make_average_surface would be useful in future.
Ju
Hi Doug,
Step 1 did not generate "/iter00/lh.reg.template.tif" - though there was
no obvious error for that on the screen. Not sure if this happened because
of not having an annot file for mris_make_template. Here is what I saw on
the screen:
%%
/usr/local/freesurfer/bin/make_average_surf
roc also spec --targ iterXX
On 09/19/2014 10:24 AM, Reza Rajimehr wrote:
> Hi,
>
> I have a question about spherical registration, and I couldn't find a
> relevant answer in the mailing list.
>
> I have two subjects S1 and S2 with corresponding functionals. I want to
&g
Hi,
I tested this with mris_convert provided by Nick in the link below, and it
worked fine.
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
However, mris_convert in dev version gave me the segmentation fault (core
dumped). Just FYI!
Best,
Reza
Hi,
To convert G
Hi,
To convert GIFTI files to the Freesurfer files, I just need to do
something like this?
mris_convert F99.R.inflated.74k_f99.surf.gii rh.inflated
Thanks,
Reza
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Hi,
I have a question about spherical registration, and I couldn't find a
relevant answer in the mailing list.
I have two subjects S1 and S2 with corresponding functionals. I want to
show the functionals of each subject on the surfaces of the third subject
S3. I have .sphere files for S1, S2, and
Hi Doug,
So I am using a command like this:
epidewarp.fsl --mag ~/MonkeyfMRI/oz_fparc/fieldmap/003/fid_mag.nii --dph
~/MonkeyfMRI/oz_fparc/fieldmap/004/fid_phasediff.nii --exf
~/MonkeyfMRI/oz_fparc/bold/template.nii.gz --exfdw
~/MonkeyfMRI/oz_fparc/bold/b0dc.nii.gz --vsm vsm.nii.gz --tediff 2.46
I forgot to mention that I want to use undistorted EPI volumes for the
functional-anatomical registration.
> Hi,
>
> I have a basic question, but the answer can be useful for others as well.
>
> I am doing a customized preprocessing of monkey functional data in FS-FAST
> v5.3. After motion correc
Hi,
I have a basic question, but the answer can be useful for others as well.
I am doing a customized preprocessing of monkey functional data in FS-FAST
v5.3. After motion correction and before functional-anatomical
registration, I want to use fieldmap data to correct spatial distortions
of EPI d
Hi,
I have got anatomicals of a subject from someone else. The anatomicals
have been processed, and the surfaces have been reconstructed. The path to
these files in my machine is obviously different from the path where data
have been analyzed. I also want to change the name of the subject and give
Hi,
I want to use FreeSurfer v5.3 and its FS-FAST for the functional analysis
of monkey data. To have a better control on the parameters of the
analysis, I prefer to run the individual commands of preproc-sess
one-by-one and check the output of each stage before proceeding with the
rest of preproc
Thanks Doug! I need to do this procedure 100 times, so I have to automate
it. Do you have an example C-shell script for this? Or is there a way to
call mri_surf2surf inside a "for loop" of Matlab?
Thanks,
Reza
not that I know of. When I have to do this, I save the data to a file,
then call mri_s
code that I can use for surface
smoothing, similar to what FS-FAST preprocessing does in Freesurfer
version 5 and above.
Thanks,
Reza
*
Reza Rajimehr, MD
Postdoctoral Research Fellow
McGovern Institute for Brain Research
Massachusetts Institute of Technology (MIT)
NMR Martinos
I have done a functional analysis for some contrasts using selxavg3-sess.
In the contrast folders, I have added some files. Now I want to do the
same analysis for some new contrasts. My guess is that selxavg3-sess
computes all the contrasts again, and I am worried that the new folders
overwrite the
Hi,
For my dataset, it appears to be easier to do an ROI analysis in Matlab
(instead of using funcroi commands). I just want to make sure the
procedure described below is right:
1) I have a label/ROI on the right hemisphere surface of a subject (e.g.
MT from the motion localizer). I convert it to
Hi,
Is there an easy way to convert a surface-based label to a mask without
going to Matlab?
Thanks,
Reza
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The information in this e
Hi,
I have two unrelated questions:
1) I have three mask files: mask1.nii.gz, mask2.nii.gz, mask3.nii.gz. The
masks might be overlapping. I want to make a new mask file in which
vertices that are 1 in mask1 or mask2 or mask3 get the value of 1, and
vertices that are 0 in all three masks get the v
as 0 in the
paradigm files.
Thanks,
Reza
*
Reza Rajimehr, MD
Postdoctoral Research Fellow
McGovern Institute for Brain Research
Massachusetts Institute of Technology (MIT)
NMR Martinos Center
Massachusetts General Hospital (MGH)
Harvard University
. How can I do this with FS-FAST/Freesurfer?
Thanks,
Reza
*
Reza Rajimehr, MD
Postdoctoral Research Fellow
McGovern Institute for Brain Research
Massachusetts Institute of Technology (MIT)
NMR Martinos Center
Massachusetts General Hospital (MGH)
Harvard University
Hi,
For a stimulus condition 'A' and a fixation condition, does the ces file
for the contrast 'A - fix' correspond to the % signal change for the
condition A?
Thanks,
Reza
****
Reza Rajimehr, MD
Postdoctoral Research Fellow
NMR Athinoul
Hi,
Using "read_curv", I load the curvature file into Matlab. How can I get
the corresponding vertex indices for these curvature values?
Thanks,
Reza
****
Reza Rajimehr, MD
Postdoctoral Research Fellow
NMR Athinoula A. Martinos Center
Department of
gt; properly?
>
> Thanks in advance
>
> Paul
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Reza Rajimehr, MD
NM
s/space/perun_004/users/sheeva/fMRIanal
>
>
>
> _______
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
vard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Reza Rajimehr, MD
NMR Athinoula A. Martinos Center
Department of Radiology
Massachusetts General Hospital (MGH)
Building 149, 1
> you used to start tksurfer?
>
> On Tue, Dec 12, 2006 at 11:28:45PM -0500, Reza Rajimehr wrote:
>> Hi (Doug, Kevin, ...),
>>
>> I am experiencing a problem with making labels in Tksurfer (for doing a
>> subsequent ROI analysis). I did something as follows:
>>
n the 2 patches. I also
had this problem before, and I am worried that some additional vertices
(voxels) are saved out of my control, which might affect the ROI analysis.
Thanks for any help,
Best,
Reza
****
Reza Rajimehr, MD
NMR Athinoula A. Martinos Center
Depar
at they are, which is a standard trick
> with the monkey data. In that case its 10 of whatever your original voxel
> dimensions were.
>
> cheers,
> Bruce
>
> On Wed, 28 Jun 2006, Reza Rajimehr wrote:
>
>> Hi,
>>
>> Does anybody have any idea what the scale b
Hi,
Does anybody have any idea what the scale bar shows in Tksurfer? I have
heard that the scalebar is 10mm for the human brain. I am working with the
monkey brain. Is the length of the scale bar 1cm for the monkey brain as
well?
Thanks,
Reza
Reza Rajimehr, MD
o the volume with mri_surf2vol.
doug
Reza Rajimehr wrote:
> Hi,
>
> Is there any way to visualize spherically-averaged maps in tkmedit-sess?
> Currently, it seems that tkmedit-sess only accepts -space native or tal.
>
> Thanks,
> Reza
***
though.
on machine monkeylove
source /usr/local/freesurfer/nmr-dev-env
setenv SUBJECTS_DIR /space/ship/3/users/reza/mvp022106/3danat
which recon-all
/usr/local/freesurfer/dev/bin//recon-all
cd /space/ship/3/users/reza/mvp022106/MYSTUDY
Thanks for any comments,
Reza
**
s?
Thanks,
Reza
****
Reza Rajimehr, MD
NMR Athinoula A. Martinos Center
Department of Radiology
Massachusetts General Hospital (MGH)
Building 149, 13th St.
Charlestown, MA 02129
Email: [EMAIL
Error in ==> /homes/4/greve/anders/recon_Monkey_fMRI.m
On line 199 ==> [kdat1,krev1,ktim1,pcdat1,pcrev1,pctim1,h1] = .. .
I do not know what this error message refers to. I would be thankful if
anyone has a suggestion.
Best Wishes,
Reza
--
****
Reza Rajimehr, M.D.
NMR
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