Postdoctoral Research Associate
Dept. of Ophthalmology and Visual science
University of Illinois at Chicago
A post-doctoral position is available in the area of Stem Cell Therapy and
Tissue Engineering at the Department of Ophthalmology. The research focuses on
generating corneal organoids
From: Avanaki, Kamran
Sent: Tuesday, February 1, 2022 5:21 PM
To: Avanaki, Kamran mailto:avan...@uic.edu>>
Subject: Postdoc position is available in Photoacoustic Imaging Instrumentation
- ASAP
Dear colleagues,
I hope you are well and safe during this complicated time.
We have a postdoc
Hello freesurfers,
I have one quick question and appreciate it very much if you could please
respond.
I have been running some resting state fmri analysis acquired on 7T scanner. In
order to do the analysis on the surface, I’ve been using "-surface self lh” for
left hemisphere analysis in
Hello,
I wanted to follow up on this question. I appreciate it much if you could
suggest me any solutions. I checked my space and I have 3.5 T free space, so
It’s definitely not a space problem.
Thanks,
Mona
On Dec 14, 2021, at 12:59 PM, Nasiriavanaki, Zahra,M.D.
mailto:znasiriavan
_
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Nasiriavanaki, Zahra,M.D.
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 12:41 PM
To:
rfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Nasiriavanaki, Zahra,M.D.
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tuesday, December 14, 2021 12:18 PM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [
output
directory?
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Nasiriavanaki, Zahra,M.D.
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Tu
-everywhere
In your case you'd replace /path/to/file with $ANTSPATH.
Anastasia.
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of N
stasia.
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Nasiriavanaki, Zahra,M.D.
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Sunday, December 5, 2021
Hello,
I’ve been running the trac-all -prep step and I faced this error:
ConvertTransformFile 3
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt
--hm --ras
ConvertTransformFile:
Hello,
I’m writing to follow up on this question. Appreciate it if you please reply.
Thanks,
Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry | MGH/HMS
149 13th Street, 149-2615
Boston, MA, USA, 02129
On Sep 30, 2021, at 8:27 PM, Nasiriavanaki, Zahra,M.D
Hi Freesurfer experts,
I was wondering how many seeds we can use in fcseedcor command? I have more
than 100 seeds and when I use all those seeds in the below command, I get this
error:
Command: fcseedcor -s $subj -fsd rest -seed 1.dat -seed 2.dat -xreg
global.waveform.dat 1 -xreg
volume?
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Nasiriavanaki, Zahra,M.D.
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Thursday, Sep
...@mgh.harvard.edu>> wrote:
What happens when you convert run 12, which has 70 volumes?
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Na
r.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Nasiriavanaki, Zahra,M.D.
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Wednesday, September 8, 2021 12:46 PM
To: Freesurfer support list
mailto:frees
Hello Freesurfers,
I have 6 runs of DTI data per subject in a sample of 50, and I want to unpack
the dicoms, so it outputs the bval bvec values, to use in dt_recon.
I realized I can use either dcm2nii or mri_convert to do this.
Could you please let me know what the command should be? and also
Dear Experts,
I have functional ROIs on the left and right hemispheres, and I’m trying to do
a bilateral seed to whole brain connectivity analysis.
My question is: in order to make a bilateral seed, shall I manually average the
.dat files (output of fcseed-sess) from left hemi and right hemi to
as all negative scalar values in it, where the default
threshold for the label is set to 0. If you set the threshold to a big negative
number it will show up.
Best,
Ruopeng
On Jul 22, 2021, at 3:35 PM, Nasiriavanaki, Zahra,M.D.
mailto:znasiriavan...@mgh.harvard.edu>> wrote:
Hello ex
Hello experts,
I am trying to load two types of labels on left hemisphere of a single subject.
In tksurfer, both labels load without an issue, but in Freeview, one type of
labels (neg.label) don’t show up. There is no error in the terminal, so I’m not
sure what’s going on.
I copied the labels
Hello Freesurferers,
I’m trying to use a functional label (extracted from task functional BOLD
data), as a seed for functional connectivity.
I tried to use the fcseed-config with -roi , but when I ran the fcseed-sess, I
got this error: “If: expression syntax error”.
Could you please let me know
Dear Freesurferers,
I have a question and I appreciate it much if you could please reply.
I need to know how to check subcortical functional to anatomical registration.
I know for checking the cortical registration I can use the below command:
tkregister2 --s $subj --mov template.nii.gz
:24 AM, Nasiriavanaki, Zahra
mailto:znasiriavan...@mgh.harvard.edu>> wrote:
Hi Doug
Thanks for your reply.
They are talairach coordinates as it is mentioned in that paper.
How may I convert the talairach to RAS?
Thanks
MOna
Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research
ystems
On 2/24/2021 3:26 PM, Nasiriavanaki, Zahra wrote:
Hi Freesurferers
I have some talairach coordinates on the cortical surface (extracted from a
paper) and I need to see their location on my fmri maps.
I used "tksurfer> go to saved point “ to see the location of that coordinate on
m
Hi Freesurferers
I have some talairach coordinates on the cortical surface (extracted from a
paper) and I need to see their location on my fmri maps.
I used "tksurfer> go to saved point “ to see the location of that coordinate on
my map.
However, that coordinate is in talairach. Should I
, MA, USA, 02129
On Jan 22, 2021, at 6:28 PM, Nasiriavanaki, Zahra
mailto:znasiriavan...@mgh.harvard.edu>> wrote:
Hi Freesurferers
I am running mri_glmfit-sim to do multiple comparison correction with the
command below. It goes through without any error. However when I view the
correcte
Dear Freesurfer experts
Hi
I was trying to measure the dimensions of a surface ROI in a flatten map on
Freeview. I used the 3D scale bar to measure the longest diameter of the ROI.
My question is how the scale bar is calculating the distance between the two
points? Is it the euclidean distance
I found the answer to my question.
Thanks anyway
Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
On Sep 10, 2020, at 6:06 PM, Nasiriavanaki, Zahra
mailto:znasiriavan
ere --sphere-center 150 138 116 --radius 5
instead of delta
On 9/10/2020 2:22 PM, Nasiriavanaki, Zahra wrote:
thanks for you reply.
So, how should I define the size of the sphere around that coordinate?
I am trying to make a subcortical 5 mm sphere ROI around that talairach
coordinate.
Thanks
Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
On Sep 10, 2020, at 1:18 PM, Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
remove --dim 5 5 5 5
this tells it to make the output volume 5 voxels
On 9/10/2020 12:53 PM, Nasiriavanaki, Zahra wrote:
Sure,
...@mgh.harvard.edu>> wrote:
please send the full terminal output
On 9/10/2020 11:24 AM, Nasiriavanaki, Zahra wrote:
Hi Doug
Thanks for your reply.
I did so, I'm getting the error below:
line 43: 8101 Segmentation fault (core dumped) mri_volsynth --template
$SUBJECTS_DIR/fsavera
below but add --delta-crsf C R S 0
where C, R, S are the col, row, slice from the voxel you found in freeview
On 9/9/2020 5:39 PM, Nasiriavanaki, Zahra wrote:
Hi
I am trying to make a subcortical 5 mm sphere ROI around a talairach
coordinate. I am using the below command, but when I visualize
Hi
I am trying to make a subcortical 5 mm sphere ROI around a talairach
coordinate. I am using the below command, but when I visualize it, it doesn’t
look at the correct location. I see the same question in forum
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67295.html), I
:56 AM, Nasiriavanaki, Zahra wrote:
Dear Freesurferers
Hi
I am trying to extract the BOLD signal values from a functional subcortical
area. I did the below steps to make the functional thalamus ROI and then used
the mri_segstats to extract the BOLD signal from it.
I would like to know 1-if my ap
Dear Freesurferers
Hi
I am trying to extract the BOLD signal values from a functional subcortical
area. I did the below steps to make the functional thalamus ROI and then used
the mri_segstats to extract the BOLD signal from it.
I would like to know 1-if my approach is correct? 2- should I use
Hi all
Please see below for available postdoc and PhD positions at the Biomedical
Engineering Department, University of Illinois at Chicago.
Best,
Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
e a paper on it
>
> On 8/7/2020 10:27 AM, Nasiriavanaki, Zahra wrote:
>> Hi Doug
>>
>> Thanks so much for your reply. This is a question that a reviewer has
>> pointed out. They were concerned that with the stimuli duration of 16 sec,
>> maybe I am not using the cor
SFAST will compute a highpass filter for
> you. I think that .01Hz is probably fine, but you could bump it up to
> .02Hz too
>
> On 8/6/2020 6:11 PM, Nasiriavanaki, Zahra wrote:
>> Hi Freesurferers
>>
>> Could you please let me know how I should calculate the
Hi Freesurferers
Could you please let me know how I should calculate the high pass filter
cutoff? I have seen a bunch of different formulas (i.e 1.5*the stimulation
period)?
My task is a block-designed task, each stimuli takes 16 seconds and is followed
by the next stimuli without an ITI.
en average them (all in mm)
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> On Behalf Of Nasiriavanaki, Zahra
> Sent: Monday, July 6, 2020 1:00 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] cortical thickness
>
> Thanks fo
mr.mgh.harvard.edu
> On Behalf Of Nasiriavanaki, Zahra
> Sent: Monday, July 6, 2020 12:31 PM
> To: Freesurfer support list
> Subject: [Freesurfer] cortical thickness
>
> Hi Freesurfer experts
>
> I have a question about the way FS calculates cortical thickness and I
>
Hi Freesurfer experts
I have a question about the way FS calculates cortical thickness and I
appreciate if you could please respond.
I calculated the cortical thickness using read_curv script in a specific ROI in
parietal lobe.
The mean thickness at that area was 2.4. Does this number show the
Hi Freesurfer experts
I have extracted the time course of a task fMRI data in a specific contrast and
within a specific ROI, in 7 subjects.
Consider my specific ROI has 1200 voxels and I extracted the time course for a
duration of 5 TRs. After extracting the timecourse, I have a matrix of
t;> wrote:
Did you pass it an analysis? There is not one in that command line
On 3/12/2020 11:28 AM, Nasiriavanaki, Zahra wrote:
Hi Freesurferers
I am trying to run selxavg3-sess for a single subject (3T fMRI data). Oddly,
the terminal output shows that it doesn't need updating for preprocessi
g like
> seg = MRIread('seg.nii.gz');
> indices= find(seg.vol == IndexOfYourROI);
> f = MRIread('f.nii.gz');
> fmat = fast_vol2mat(f);
> froi = fmat(:,indices);
>
> this assumes taht f.nii.gz and seg.nii.gz are in vox-for-vox registration
>
>
>
> On 3/18/2020 5
Hi all
Is there any command for extracting the fmri activation from all voxels in an
ROI?
I know I can use funcroi-config, funcroi-sess and funcroi-table-sess to extract
the average activation in a specific ROI from a specific contrast. But what if
I want to extract the values of each voxel
id you pass it an analysis? There is not one in that command line
On 3/12/2020 11:28 AM, Nasiriavanaki, Zahra wrote:
Hi Freesurferers
I am trying to run selxavg3-sess for a single subject (3T fMRI data). Oddly,
the terminal output shows that it doesn't need updating for preprocessing and
Hi Freesurferers
I am trying to run selxavg3-sess for a single subject (3T fMRI data). Oddly,
the terminal output shows that it doesn't need updating for preprocessing and
ends with this: "Started at Thu Mar 12 10:48:09 EDT 2020
Ended at Thu Mar 12 10:48:12 EDT 2020 preproc-sess done". It
PM, Nasiriavanaki, Zahra
mailto:znasiriavan...@mgh.harvard.edu>> wrote:
Hi Freesurferes
I have extracted timeseries from a task fMRI using the command below:
mri_segstats --i fmcpr.sm0.self.rh.nii.gz --slabel $subj rh rh.label --id 1
--avgwf-remove-mean --avgwf ./rh.txt
My qu
Hi Freesurferes
I have extracted timeseries from a task fMRI using the command below:
mri_segstats --i fmcpr.sm0.self.rh.nii.gz --slabel $subj rh rh.label --id 1
--avgwf-remove-mean --avgwf ./rh.txt
My question is: Is the temporal drift being counted in considering that I used
preprocessed
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Nasiriavanaki, Zahra
Sent: Wednesday, February 19, 2020 10:27 AM
To: Greve, Douglas N.,Ph.D. ;
freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glmfit --no-prune
Dear Doug
Thanks a lot for your
specify --wls, it normalizes the weights across subject. However,
in the medial wall, all the weights are 0 (can't divide by 0, so it throws an
error.
On 2/18/2020 5:35 PM, Nasiriavanaki, Zahra wrote:
Hi Freesurferers
I am running mri_glmfit on a group data using --no-prune flag. i 'm getting
Hi Freesurferers
I am running mri_glmfit on a group data using --no-prune flag. i 'm getting the
below error.
I appreciate if you could let me know what the issue is.
Loading y from
/autofs/space/oprah_001/users/zn025/looming_3T/group_levels/patients_20/loom.lh/aw/ces.nii.gz
... done
From: Nasiriavanaki, Zahra
Sent: Monday, February 10, 2020 12:11 PM
To: Freesurfer support list
Subject: make average subject/ highres fMRI data
Dear Freesurfer experts
Hi
I got an error when I was trying to make an average subject. I attached the log
file.
I
Dear Freesurfer experts
Hi
I got an error when I was trying to make an average subject. I attached the log
file.
I appreciate if you could please let me know what the problem is.
make_average_subject --out avgsubject --subjects subj1 subj2 subj 3
labeling Slice
relabeling unlikely voxels in
Dear Freesurfer experts
I want to extract "activation timeseries (BOLD signal changes in each time
point) " from a predefined ROI in a single subject task fMRI data. Previously,
I extracted these values from fmcpr.sm0.self.lh.nii.gz by using mri_segstats,
but the data seems to be too noisy.
---
ERROR: fast_selxavg3() failed\n
Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
From: Nasiriavanaki, Zahra
om as well as the $SUBJECTS_DIR
On 8/5/2019 1:33 PM, Nasiriavanaki, Zahra wrote:
Thanks for your reply.
preproc-sess -s $subj -per-run -nostc -fwhm 0 -surface fsaverage lhrh -fsd bold
-init-header -d .
Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachuset
From: Greve, Douglas N.,Ph.D.
Sent: Thursday, January 2, 2020 3:25 PM
To: Nasiriavanaki, Zahra ;
freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] highres fMRI selxavg error
It appears to be dying on this command
mris_fwhm --mask
/autofs/space/oprah_001/users/zn025
for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
From: Greve, Douglas N.,Ph.D.
Sent: Thursday, January 2, 2020 1:18 PM
To: Nasiriavanaki, Zahra ;
freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer
pital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
From: Greve, Douglas N.,Ph.D.
Sent: Thursday, January 2, 2020 11:46 AM
To: Nasiriavanaki, Zahra ;
freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] highres fMRI selxavg error
When you say you n
selxavg error
Why are you combining them into one bold folder?
On 12/30/2019 9:09 AM, Nasiriavanaki, Zahra wrote:
Dear Freesurfer experts
Happy Holidays!
I have a subject with two highres fMRI scan sessions. Attached you can see an
image, showing how I organized the sub-folders.
I preprocessed
/stable6/bin/recon-all.v6.hires:
Permission denied
Zahra (Mona) Nasiriavanaki
Postdoctoral Research Fellow
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129
From: Nasiriavanaki, Zahra
ch I
created the HCP. If you are in the version 6 environment, you can run
recon-all.v6.hires the same way you did recon-all, but do not use -hires
and instead use -conf2hires
doug
On 12/9/19 6:17 PM, Nasiriavanaki, Zahra wrote:
> Dear Freesurfer experts
>
> Hi
>
> I have a follow
lts.
doug
On 12/11/19 11:30 AM, Nasiriavanaki, Zahra wrote:
> Dear Freesurfer experts
>
> Hi
>
> I was trying to do selxavg in native space for individual subjects
> which I have analyzed them in "fsaverage" space before.
> I have two sessions of functional data for
Dear Freesurfer experts
Hi
I was trying to do selxavg in native space for individual subjects which I have
analyzed them in "fsaverage" space before.
I have two sessions of functional data for each subject. In order to register
them on one T1, I put the functional data from both sessions in
ed to look at it to tell. Have you flattened other
subjects successfully?
cheers
Bruce
On Fri, 8 Nov 2019, Nasiriavanaki, Zahra
wrote:
> Hi Freesurfer experts
>
> I was trying to make flat maps for individual subjects, following instruction
> in
> https://surfer.n
) replace 'fsaverage' with the subject identifier in the command, e.g.:
tksurfer subject23 lh inflated -ov sig.nii.gz
Best,
Tim
> On October 28, 2019 at 3:21 PM "Nasiriavanaki, Zahra"
> wrote:
>
>
> Hi Doug
>
> Thanks for your reply.
> Could you pleas let
ect do not have any correspondence to vertices in
an other subject
On 10/25/19 12:08 PM, Nasiriavanaki, Zahra wrote:
Hi Freesurfer experts
I have a few labels that correspond to activation clusters in fsaverage space
for an individual subject. I used mri_label2label to transfer them to native
Hi Freesurfer experts
I have a few labels that correspond to activation clusters in fsaverage space
for an individual subject. I used mri_label2label to transfer them to native
space of the subject.
export SUBJECTS_DIR=/autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR
mri_label2label
Hi Doug
I wanted to follow up this email and ask you a question. I see in the fspalm
page, it says "You can use fspalm with both volume- and surface-based analyses;
it will figure everything out".
Considering your reply to the below email, I'm wondering if we can use fspalm
for subcortical
/FsFastParametricModulation
On 9/13/19 11:08 AM, Nasiriavanaki, Zahra wrote:
Dear Freesurfer experts
Hi
I have a question about weighting different contrasts using mkcontrast-sess
commmand.
I have single subject functional data with 18 different contrasts, and I am
willing to weight the different contrasts
From: Nasiriavanaki, Zahra
Sent: Friday, September 13, 2019 11:08 AM
To: Freesurfer support list
Subject: mkcontrast-sess question
Dear Freesurfer experts
Hi
I have a question about weighting different contrasts using mkcontrast-sess
commmand.
I have single subject
Dear Freesurfer experts
Hi
I have a question about weighting different contrasts using mkcontrast-sess
commmand.
I have single subject functional data with 18 different contrasts, and I am
willing to weight the different contrasts as (for example) ascending linear.
Something like:
e power.
On 9/10/19 11:35 AM, Nasiriavanaki, Zahra wrote:
> Hi Doug
>
> Thank you very much for your reply. How does it make a difference if I
> use FIR? Could you please explain a little bit more?
>
> Thanks
> Mona
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctor
to assume a shape to the hemodynamic response, then I
don't think it makes much difference. It will make a difference if you
are going to use an FIR.
On 9/9/19 10:49 AM, Nasiriavanaki, Zahra wrote:
> Hi Freesurfer experts
>
> I have a question about designing an event related task. We are
&g
Hi Freesurfer experts
I have a question about designing an event related task. We are designing a
task for fear conditioning. Each stimuli presentation lasts 4 seconds. My
question is if we set the TR to 2 (which is a multiply of 4), will it make the
paradigm to have more power in signal
AM, Nasiriavanaki, Zahra
mailto:znasiriavan...@mgh.harvard.edu>> wrote:
Hi Ruopeng
Thanks for your reply.
I have a question though. When I zoom in the 3D image, the scale bar numbers
don't change. Shouldn't they change when I zoom in?
Thanks
Mona
Zahra (Mona) Nasiriavanaki
Postdoctoral Re
question
Hi Mona,
If you are running the latest dev build, you can right click in the 3D view and
choose “Show 3D scale”. The scale bars can only be placed at the boundary of
the FOV.
Best,
Ruopeng
On Aug 15, 2019, at 4:30 PM, Nasiriavanaki, Zahra
mailto:znasiriavan...@mgh.harvard.edu>>
tial scale bar question
Hi Mona
sure. As I said it is a bit more complicated than it seems. Ruopeng will
post a note when something usable is in the dev version
Bruce
On Mon, 13 May
2019, Nasiriavanaki, Zahra wrote:
>
> Yes Bruce.
>
> It doesn't work.
>
> I appreciate if you co
?
On 8/2/2019 12:17 PM, Nasiriavanaki, Zahra wrote:
Dear Freesurfers
Hi
I have a subject that the registration is not done correctly in two runs (run
12 and run 15) .
The tkregister-sess values for this subject is shown below.
Subject 1 10 0.2628
Subject 1 11 0.3038
Subject 1 12 0.7639
Subject
From: Nasiriavanaki, Zahra
Sent: Friday, August 2, 2019 12:17:53 PM
To: Freesurfer support list
Subject: mis-registration question
Dear Freesurfers
Hi
I have a subject that the registration is not done correctly in two runs (run
12 and run 15) .
The tkregister-sess values for this subject
Dear Freesurfers
Hi
I have a subject that the registration is not done correctly in two runs (run
12 and run 15) .
The tkregister-sess values for this subject is shown below.
Subject 1 10 0.2628
Subject 1 11 0.3038
Subject 1 12 0.7639
Subject 1 13 0.3364
Subject 1 14 0.3346
Subject 1 15
y have a small slab of brain in the fMRI. What am I missing?
On 6/28/2019 10:41 AM, Nasiriavanaki, Zahra wrote:
Thank you so much for your reply.
I attached new images.
I scrolled through the brain and the worst registration is the last image
attached.
I'm wondering what else could cause high
Dear Freesurfer experts
Hi
I was wondering how should I cite the Freesurfer QA_tools in a paper. I
couldn’t find any references in the web page
(https://surfer.nmr.mgh.harvard.edu/fswiki/QATools).
Thanks
Mona
___
Freesurfer mailing list
No, you'll need to change your paradigm file to have two distinct 8 sec
events rather than one 16 sec event.
On 5/20/19 10:12 AM, Nasiriavanaki, Zahra wrote:
>
> Hi Freesurfer experts
>
>
> I am making an analysis in Freesurfer version 6 and I have a question
> abou
Hi Freesurfer experts
I am making an analysis in Freesurfer version 6 and I have a question about the
"refeventdur" in mkanalysis-sess command.
My stimulus duration is 16 seconds, but for a specific analysis, I only want to
include half of the stimulus duration (ex: the first 8 seconds only
Great!
Thanks
> On May 13, 2019, at 9:56 AM, Bruce Fischl wrote:
>
> Hi Mona
>
> sure. As I said it is a bit more complicated than it seems. Ruopeng will post
> a note when something usable is in the dev version
>
> Bruce
>
>
> On Mon, 13 May 2019, Nasi
/greve/fv.colorbar.gif
[https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif]
>
>
> On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:
>
> Thanks for your reply.
>
> I have overlaid the significance map on an inflated brain, and I don't
> see the s
.
Sent: Friday, May 10, 2019 3:27:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] spatial scale bar question
In freeview, it is just an icon above the image window. Click on it and it
should give you a scale bar
On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:
Dear Freesurfers
Dear Freesurfers
Hi
I am trying to add a spatial scale bar to my cortical maps in tksurfer.
However, as it's mentioned in Freesurfer forum before, the scale bar in
tksurfer shrinks when you zoom in the brain.
I couldn't find a scale bar option in Freeview neither.
I appreciate if you could
Dear Freesurfer experts
Hi
I have a question about funcroi-table-sess, and I appreciate if you could
please find a time to reply.
Is there anyway that funcroi-sess-table can give out the activation values in
each timepoint separately? Right now I can get the average of activation in
each
From: Nasiriavanaki, Zahra
Sent: Thursday, April 11, 2019 4:52:49 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_segstats
Thank you so very much.
Yes, the values look normal now.
Mona
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of G
] mri_segstats
You probably need to remove the mean. Add --avgwf-remove-mean to the
command line
On 4/11/19 4:29 PM, Nasiriavanaki, Zahra wrote:
>
> Thank you for your reply.
>
> The values of mri_segstatsoutput text file (lateral.txt) are high. I
> attached it to this email.
>
&g
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Greve, Douglas N.,Ph.D.
Sent: Thursday, April 11, 2019 4:19:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_segstats
The value of what is too high?
On 4/11/19 4:07 PM, Nasiriavanaki, Zahra
Hi
I have not got the answer to my question yet, and I appreciate if you could
please let me know what you think about it.
Thanks
Mona
From: Nasiriavanaki, Zahra
Sent: Tuesday, April 9, 2019 5:55:58 PM
To: Freesurfer support list
Subject: mri_segstats
Dear
Dear Freesurferers
I was trying to do a connectivity analysis using subnuclei of Amygdala.
I had an Amygdala segmentation file (reg.lh.HBT.mgz for letf Amygdala) and I
tried to use that in mri_segstats to extract the timeseries and then use it as
a seed in my analysis. However when I looked
: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Nasiriavanaki, Zahra
Sent: Wednesday, March 27, 2019 4:44:14 PM
To: Freesurfer support list
Subject: [Freesurfer] exact time of data acquisition per run
ATTENTION: This email came from an external source. Do not open attachments or
click on links
Dear Freesurfer experts
Hi
I am trying to extract the time of data acquisition for each run from the
functional data and compare it with my paradigm files.
I thought the numbers in DICOM file names (ie,
MR.1.3.12.2.1107.5.2.43.67026.2019011316475911712728505 ) are correspondent
with the
: [Freesurfer] tkregister-sess
Did you delete the bad registration file and re-run the registration
(preproc-sess)?
On 3/18/19 11:53 AM, Nasiriavanaki, Zahra wrote:
Dear Freesurfers
Hi
I was checking the functional on structural data registration quality by using
the below command.
tkregister-sess
Dear Freesurfers
Hi
I was checking the functional on structural data registration quality by using
the below command.
tkregister-sess -s $subj -fsd bold -per-run -bbr-sum
I observed high values (around 0.9) for one of my subjects, and I figured out,
that subject was registered to another
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