.fsaverage.?h.nii.gz and fmcpr.odd.sm5.mni305.2mm.nii.gz)
into CIFTI format?
-Sabin
On Tue, Sep 13, 2016 at 3:09 PM Sabin Khadka <mr.sabinkha...@gmail.com>
wrote:
> Hi Doug- I did try
> mris_convert -o $SUBJECTS_DIR/FSsub/surf/lh.white
> $SUBJECTS_DIR/sub/REST/bold/001/fmcpr.odd.sm5.fsav
Hi Doug- I did try
mris_convert -o $SUBJECTS_DIR/FSsub/surf/lh.white
$SUBJECTS_DIR/sub/REST/bold/001/fmcpr.odd.sm5.fsaverage.lh.nii.gz
fmcpr.lh.gifit-file.gii
I still get freadFloat: frear failed error.
Cheers,
Sabin Khadka
On Tue, Sep 13, 2016 at 2:53 PM, Douglas N Greve <
Hi all,
Is there a way to convert FSFAST files (fmcpr.odd.sm5.fsaverage.?h.nii.gz)
files to convert into gifti format? I've tried mris_convert but it does not
work.
Thanks for help.
Cheers,
Sabin Khadka
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Hi Michael- Thanks very much for the file. Is there published paper or
other documents that I could use as reference for these annotation?
Cheers,
Sabin Khadka
On Wed, Aug 17, 2016 at 12:53 PM, Harms, Michael <mha...@wustl.edu> wrote:
>
> They are attached (assuming that the FS
Hi Michael- Is there anyway I can get those Gordon parcellation annot files?
Cheers,
Sabin Khadka
On Wed, Aug 17, 2016 at 10:59 AM, Harms, Michael <mha...@wustl.edu> wrote:
>
> FYI: I supplied a version of the “Gordon” parcellation in .annot format to
> Bruce a while back. H
Hi Doug- Do you think it is possible to use these atlas? If so could you
point me to steps that needed to be done.
Thanks for your help!
Cheers,
Sabin Khadka
On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> I have not used them myself.
>
> O
please advise me on how do it (if they are at all possible).
Cheers,
Sabin Khadka
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Anyone?
Cheers,
Sabin Khadka
On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka <mr.sabinkha...@gmail.com>
wrote:
> Hi Doug, I tried to pick up from the thread below to get MNI coordinates
> of each destrieux parcellation region.
>
>
>
> https://mail.nmr.mgh.harvard.edu/pi
Hi Doug, I tried to pick up from the thread below to get MNI coordinates of
each destrieux parcellation region.
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html
I created label files from
mri_annotation2label --subject fsaverage --hemi lh(/rh) --annotation
.nii.gz --ctab
$FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/Yeo2011_7Networks_ColorLUT.txt
--excludeid 0 --i fmcpr.anat.nii.gz --avgwf Cerebellum_networks_R.txt #
extract right Cerebellum time series
Cheers,
Sabin Khadka
On Tue, Jul 5, 2016 at 3:48 PM, Douglas N Greve <
Hi Thomas- On second thought is it valid to simply do if I want average
time series of the cerebellum regions?
fslmeants -i fmcpr.anat.nii.gz -m Buckner_atlas_FSSub.nii.gz >>
avgCerebellum.txt
Is this correct?
Cheers,
Sabin Khadka
On Mon, Jun 27, 2016 at 11:36 AM, Sabin Khadka <mr
doing anything wrong here. Do you have any suggestions/fixes?
Cheers,
Sabin Khadka
On Fri, Jun 24, 2016 at 6:30 AM, Thomas Yeo <ytho...@csail.mit.edu> wrote:
> Hi Doug, thanks.
>
> Hi Sabin, you can use the following steps to transform the Buckner
> cerebellum atlas to you
? or if I have to use some other scripts commands (other
than mri_segstats).
Cheers,
Sabin Khadka
On Mon, Jun 20, 2016 at 10:20 PM, Thomas Yeo <ytho...@csail.mit.edu> wrote:
> Hi Sabin,
>
> The structures 601-628 FreeSurferCololLUT.txt correspond to anatomical
> substructures of t
exactly to extract time series from cerebellar
regions. So if I want to extract time series from regions as described in
Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628 in
FreeSurferCololLUT.txt? If not could you please direct me to processes that
I can use.
Cheers,
Sabin
Hi all,
I am trying to extract mean time series BOLD data using FSFAST from Cortical
ROIs + sub cortical ROIs and cerebellum.
preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6
-per-run -stc odd mri_segstats --annot fsaverage lh aparc --i
Hi all,
I used FDR correction method to correct for multiple comparison after
mri_glmfit. And I have a cluster covering multiple regions. I want to extract
the thickness, surface area, lgi values for local maxima (or, multiple regions
covered by the big significant cluster). I see it is not
Hi all - When you get a significant cluster after doing monte-carlo simulation,
we get peak vertex/Talairach coordinates and also saved in *summary files. Is
there a way to find all the parcellated regions (Desikan, or, Destriuex) in the
significant clusters?
Hi all - When you get a significant cluster after doing monte-carlo simulation,
we get peak vertex/Talairach coordinates and also saved in *summary files. Is
there a way to find all the parcellated regions (Desikan, or, Destriuex) in the
significant clusters?
Thanks,Sabin
Hi all - When you get a significant cluster after doing monte-carlo simulation,
we get peak vertex/Talairach coordinates and also saved in *summary files. Is
there a way to find all the parcellated regions (Desikan, or, Destriuex) in the
significant clusters?
Thanks
Hi all,If I understand correctly, preproc-sess command takes mid point of EPI
image as reference and make template and calculate motion parameters. I could
not figure if I could use different image as reference, is it possible?
Cheers,
Sabin Khadka___
Hi all- Is there a command we can have screenshots (similar to one employed in
fsl) of fucntional-- structural registration in FSFAST to visually check the
registration on top of the BBR cost?
Cheers,
Sabin Khadka
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Hi FS Users,
I've preprocessed resting state fmri data using preproc-sess as shown in FSFAST
functional connectivity walk through manual. I know I can extract mean time
series of a seed region using fcseed-sess. I am trying to find a command to
extract mean time series from all Desikan (or
doingmri_segstats --seg fsaverage/mri/aseg.mgz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --avgwf test2.txtbut it gave me
dimension mismatch error. I'd appreciate if you'd direct me on how to get
average time series values from subcortical regions.
Cheers,
Sabin Khadka
From: Douglas Greve gr
Hi Doug- Works fine. I appreciate your help.
Related but different question: Would you help me understand how the QA
value(0-1)while checking registration using following command is calculated.
tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum
Cheers,
Sabin Khadka
Hi Doug- The command doesn't error out but it just give me one value. I was
assuming the following command would give me value in time series x mean value
in text file. Am I following correct strategy/commands? Cheers,
Sabin Khadka
From: Douglas Greve gr...@nmr.mgh.harvard.edu
To: sabin
Works fine. thanks for the help Doug. Cheers,
Sabin Khadka
From: Douglas Greve gr...@nmr.mgh.harvard.edu
To: sabin khadka sabink...@yahoo.com; Freesurfer support list
freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, January 27, 2015 12:33 PM
Subject: Re: [Freesurfer] Extract mean time
/aparc+aseg.mgz
--reg register.dat --o test2.nii.gzEPI.nii.gz is 4D image with 210 frames. How
can I get test1.nii.gz and test2.nii.gz in 4D format? Should be something basic
but I could not figure out how.
I appreciate your help!!
Cheers,
Sabin Khadka
From: Douglas Greve gr
Hi FS user,
I am trying to extract time series of fmri rest data of certain parcellated
regions (both cortical and subcortical). for that I am doing following
# bbregister --s sub id --mov EPI.nii.gz --init-fsl --reg register.dat
--bold# mri_label2vol --aparc+aseg --subject sub id --temp
Hi FS users,
We've T1 and EPI images collected. For my analysis I want to use FS parcellated
regions (both cortical/sub-cortical regions) as ROIs (Masks) for my functional
images. Would anyone kindly let me know what is the best way to proceed. Cheers,
Sabin
Hi Doug- Thanks for the reply. Would you mind elaborating on how exactly to use
mri_label2vol to map the aparc+aseg.mgz into the
function space ( I could not find the correct syntax that should be used)?
Also, what should i do if I want individual masks for each ROI?
Cheers,
Sabin Khadka
Hi all,
I am trying to run 2x3 factorial model correcting for age, sex and intracranial
volume. Just to give you insight in my data I have my fsgd file as
GroupDescriptorFile 1
Title DOSS analysis 2x3 factorial
Class MaleGroup1Low
Class MaleGroup1Medium
Class MaleGroup1High
Class MaleGroup2Low
Hi all,
I want to extract to extract thickness, area and lgi values vertex wise
in ascii files for group of subjects. Could anyone suggest me on how to do it.
Thank you for your help.
-Sabin___
Freesurfer mailing list
a 5 column ascii file in the format
vertex index x y z thickness
cheers
Bruce
On Thu, 17 Apr 2014,
sabin khadka
wrote:
Hi all,
I want to extract to extract thickness, area and lgi values vertex wise in
ascii files for group of subjects. Could anyone suggest me on how to do it.
Thank you
, sabin khadka sabink...@yahoo.com wrote:
Ahh. Great. Thanks you very much for the information.
I ran mri_surf2surf and then mris_convert to get thickness and surface area
vertex wise values. I found that some vertices had negative values of surface
area for few subjects. Should not surface area
Hi all,
Related question to this.
I am trying to extract vertexwise surface area values in an ascii files. For
that I am doing
mri_surf2surf
--hemi ?h --srcsubject subject dir area --src_type curv
--trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv
mris_convert -c XYZ-area ?h.white
it?
Thanks,
Sabin
On Tuesday, April 15, 2014 11:29 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
what is your command line? The one below is not a valid command line.
On 04/15/2014 11:23 AM, sabin khadka wrote:
Hi all,
Related question to this.
I am trying to extract vertexwise
Hi all,
I am trying to extract vertexwise surface area values in an ascii files. For
that I am doing
mri_surf2surf
--hemi ?h --srcsubject subject dir area --src_type curv
--trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv
mris_convert -c XYZ-area ?h.white XYZ-area.asc
However I am
Hi all,
I am trying to extract vertexwise surface area values in an ascii files. For
that I am doing
mri_surf2surf
--hemi ?h --srcsubject subject dir area --src_type curv
--trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv
mris_convert -c XYZ-area ?h.white XYZ-area.asc
However I am
-
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Sorry all. Just a test e-mail.
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addressed. If you
Hi all,
I am trying to extract vertexwise surface area values in an ascii files. For
that I am doing
mri_surf2surf
--hemi ?h --srcsubject subject dir area --src_type curv
--trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv
mris_convert -c XYZ-area ?h.white XYZ-area.asc
However I am
Hi all,
I am trying to extract vertexwise surface area values in an ascii files. For
that I am doing
mri_surf2surf --hemi ?h --srcsubject subject dir area --src_type curv
--trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv
mris_convert -c XYZ-area ?h.white XYZ-area.asc
However I am
compare the aseg.stats file to see which segs are missing.
doug
On 3/2/14 9:46 AM, sabin khadka wrote:
Hi all,
While using asegstats2table, I got following error for few subjects,
WARN SUBID: nmeasure 66, expecting 55
It let me extract cortical thickness and surface area using
Hi all,
While using asegstats2table, I got following error for few subjects,
WARN SUBID: nmeasure 66, expecting 55
It let me extract cortical thickness and surface area using aparcstats2table
though.
Any suggestions?
-SABIN___
Freesurfer mailing list
Hi all,
I ran recon-all -all and all the subjects finished without any error. However
in few subjects directory, labels sub-directory only have lh.cortex.label and
rh.cortex.label and not other label files like *.label and *.annot. Could
anyone help me on how to fix this.
Hi all,
I am trying to run fReadQdec.m. My qdec.table.dat file is a tab delimited file.
However when it reads to Qdec variable it reads it as N(# of subjects)X1 cell
(discounting for all tabs and spaces). I tried debugging the code but it seems
to me like it is just a simple read file in
for each variable that I
put in table).
-Sabin
On Tuesday, February 18, 2014 1:26 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
yes, it has a certain format. Look at the examples on the wiki
doug
On 02/18/2014 11:19 AM, sabin khadka wrote:
Hi all,
I am trying to run fReadQdec.m. My
did you get this m file from? I don't see it in our distribution.
On 02/18/2014 03:29 PM, sabin khadka wrote:
Hi Doug,
Thanks for the reply. Yeah I have my qdec.table.dat file in the same
format as wiki says and in tab delimited format. But when I try to run
fReadQdec it reads it as N
Hi all,
I was just wondering if there is a tutorial or example on how to use
linear mixed effect model toolbox for longitudinal analysis.
I already processed my structural images with longitudinal processing pipeline
from freesurfer. I want to do group analysis where I have 4 groups with
Hi all,
Just to be sure, if I want to compare ICV or hippocampus volume between two
time points I extract the values from aseg.stats of MRI_001.long.template
and MRI_002.long.template right. Also, if thats the case is it okay if I
rerun autorecon with -hippo-subfields flags for those
Hi all,
I am trying to use qdec to perform comparison of cortical thickness in two
different time periods. So I ran recon-all base and recon-all -long. then
defined long.qdec.table.dat as
fsid fsid-base years
MRI_001_T1 MRI_001 0
MRI_001_T2 MRI_001 2
When I
HI all,
I ran longitudinal processing with
reco-all -base templateID -tp MRI_T1 -tp MRI_T2 -all
but in base-tps file of template ID I found the subject ID of MRI_T1 twice
instead of MRI_T1 and MRI_T2. I want to run recon-all -long which I am able
to do for MRI_T1 but could not do the same for
Hi all,
Is there a longitudinal processing stream to compare local gyrification
index (lgi) across two time points.
-Sabin
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The
Hi all,
What does -washu_mprage and -mprage flags do in autorecon step. How does it
help in segmentation?
-SK
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The information in
Hi Michael,
I had the same problem too. It might be because of the type of scanner you
are using. I added -washu_mprage flag, it pretty much helped me (I did not
had to add a lot of controls points and so on so forth. You can go through
the link below.
Dear all,
Is there any documentation on doing em edit using freeview.
Thanks,
SK
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