External Email - Use Caution
Thank you so much. Now I at least get a direction from where to start.
Regards:
Rahul Sharma
Research Scholar
NIT Silchar
Assam
9827834360
*"Manners Maketh Man"*
On Wed, Jan 18, 2023 at 5:36 PM Marina Fernández <
marina.fdez.alva
External Email - Use Caution
Hello Mam,
I am not replying to your mail, instead I need to know the source where you
learn Freesurfer and pre processing of MRI and PET.
Please do reply.
On Tue, 17 Jan 2023, 11:16 pm Marina Fernández, <
marina.fdez.alva...@gmail.com> wrote:
>
External Email - Use Caution
Hello everyone, I am very new to this neuroimaging and belongs to technical
background. Could anyone provide me any source or material for
understanding MRI scans and the neuroimaging tools such as Freesurfer or
FSL. Eagerly waiting for your reply.
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From where I will get the freesurfer course materials. as I am unable to
purchase the course.
Please help me out in this regard.
Regards:
Rahul Sharma
*"Manners Maketh Man"*
On Thu, May 26, 2022 at 7:04 PM Kretzer, Sve
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Has anyone ever downloaded ADNI dataset for AD diagnosis?
Please let me know.
Regards:
Rahul Sharma
Research Scholar
*"Manners Maketh Man"*
On Wed, Apr 13, 2022 at 4:03 PM Joana Braga Pereira
wrote:
> External Email
Hi FreeSurfer experts,
I have a dataset of 60 patients. Is there a way to visualize the average
cortical thickness/area for my dataset?
Thank you in advance.
Rahul
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Freesurfer@nmr.mgh.harvard.edu
https
) using freesurfer?
Thank you,
Rahul
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you
am not sure
why recon-all is existing for freesurfer 7.2 and how can I stop that.
Thank you
Rahul
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Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is
am not sure
why recon-all is existing for freesurfer 7.2 and how can I stop that.
Thank you
Rahul
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The information in this e-mail is
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I want Susceptibility Weighted and T1 weighted MRI scans for neurological
disorder. Any help how we can get the data.
Please help us out.
On Sat, 17 Jul 2021, 3:29 pm AmirHussein Abdolalizadeh, <
amirhussei...@gmail.com> wrote:
> External Ema
--cwp 0.05
--2spaces
How can I fix the error?
Thank you,
Rahul
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Hi,
Hope all are safe and well. Can anyone help me in finding any biomarker for
Alzheimer's Disease or any guidance related to that?
Waiting for response.
Regards:
Rahul Sharma
Research Scholar
9827834360
*"Manners
Hi Bruce,
Is it possible to do a zoom call for troubleshooting with me and my PI today?
Rahul
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Fischl, Bruce
Sent: Friday, January 29, 2021 12:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re
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Dear All,
Hope everyone is safe and well.
Did anyone you have MNI152 TEMPLATE mainly required for Alzheimer's
Diagnosis.
Also can anyone help in recommending any tool other than FREESURFER for
preprocessing of sMRI scans for Alzheimer's disease but the
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Any tools other than Freesurfer for preprocessing Nifti sMRI scans. Only
requirement is it should work on windows.
On Thu, 17 Dec 2020, 4:22 pm Laura f, wrote:
> Dear Sir or Madam,
> I am not longer working with FreeSurfer so I would like to remove m
to be extracted but for some images they are
similar but for most of the images the extracted slice is different.
Regards:
Rahul Sharma
Research Scholar
NIT Silchar
Assam
9827834360
*"Manners Maketh Man"*
On Sun, Oct 11, 2020 at 8:46 PM Fischl, Bruce
wrote:
> Hi Rahul
>
> can you
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Dear all,
Hope you all are in good health, I want to ask that how I can reslice the
two different MRI scans so that when I extract the sagittal slices it all
look same, can you help me out
Regards:
Rahul Sharma
Research Scholar
NIT Silchar
Assam
External Email - Use Caution
Hello Freesurfer user,
I am very much new to the use of freesurfer. Can anyone share from where to
study so that I can start using freesurfer.
I basically wants to extract hippocampus trophies and GM WM CSF volumes
Regards:
Rahul Sharma
+91
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Thanks, I'll check it out.
Regards:
Rahul Sharma
Research Scholar
NIT Silchar (Assam)
9827834360
On Fri, 12 Jun 2020, 2:03 am fsbuild, wrote:
> Hello Rahul,
>
> Did you try following the instructions on the wiki pages about how to d
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Unable to perform installation. Please help me out regarding the same.
Regards:
Rahul Sharma
Research Scholar
NIT Silchar (Assam)
9827834360
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https
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Can anyone please help me out which OS will be suitable for using
freesurfer from now onwards.
Regards:
Rahul Sharma
Research Scholar
NIT Silchar (Assam)
9827834360
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Freesurfer
Hi Ruthger,
The temporal lobe list/label should include the banks of the superior
temporal sulcus (bankssts). Not sure why it's not in there but we will
include it. Thanks for pointing this out!
Best,
Rahul
> Dear Freesurfers,
>
> I would like to do Lobe mapping, based on the De
every
individual subject.
Hope this helps,
rahul
> Hi Fatima,
>
> it's kind of a poorly-defined region, so I'm not sure how to answer.
> Those labels don't make up all of prefrontal cortex. Maybe the easiest
> thing to do is to draw it yourself on fsaverage
Hi Narly,
You can take a look at the Desikan et al. 2006 paper for boundary
definition for the transverse temporal gyrus.
Best,
Rahul
>
> Hello,
>
> I would like to know more about the automatic labelling of the transverse
> temporal gyrus is done. I looked at the below articl
Hi Stephen,
For the ?h.aparc.annot atlas, the boundary definitions are included in the
Desikan et al., 2006 paper (Neuroimage).
Best,
Rahul
> One of the regions we are investigating using a surface-based analysis is
> the anterior cingulate. In some of our surface reconstructions, pa
s
the insular cortex -- for more details on how the wm and gm are segmented,
please see Fischl et al., 1999, 2002.
Hope that helps,
rahul
> Hi Seyed,
>
> I don't think there's any easy adding up of labels that gives you the
> temporal lobe, but Rahul and/or Christophe can cor
Hi Falk,
We do indeed have cortical thickness values for each of the parcellation
units for a range of subjects (healthly elderly, middle age and young
controls and Alzheimer's disease subjects). Which parcellation units are
you looking for? A whole lobe?
Best,
rahul
> Hi Falk
tly.
Hope this helps.
Best,
Rahul
--
Rahul S. Desikan
ra...@nmr.mgh.harvard.edu
> Hi,
> I have an area of significance on the mesial surface of the hemisphere
> (please see attached tiffs). I would like to know if it is exclusively in
> the cingulate or in cingulate and SFG. The prol
e get mean thickness of 3.11
for left and 3.10 for right temporal pole.
Hope this is helpful.
Best,
rahul
> Many thanks for your e-mail, Bruce.
>
> Yes, I've inspected all data, and one of the things that makes me more
> worried is that I had to edit many subjects in this area bec
Hi Vina,
This label corresponds to the posterior banks (posterior to the tranverse
temporal gyrus) of the superior temporal sulcus.
cheers,
rahul
> Hi guys,
> In the freesurfer aparc.annot label what is the "banksst" region in
> the temporal lobe?
group comparisons, not indidividual subject morphometric information, and
does not allow you to either predict or longitudinally track morphometric
changes in a single individual.
Hope this helps,
Rahul
--
Rahul S. Desikan
[EMAIL PROTECTED]
> Gentlemen,
>
> I am giving a lecture about aging
Hi Mike,
As Bruce mentioned, I did some fixes in the manual parcellations which
affects the aparc atlas in addition to the changes he made.
Best,
rahul
> both I think. Rahul fixed some thinks in the manual parcellations, and I
> passed the aseg to mris_ca_label so it could tell if s
Hi Mike,
The mislabelling was primarily for the surface parcellations (aparc) but I
think it would also affect the asegs as well.
Best,
rahul
>
> Hi Rahul,
> Was that mislabeling of rostral anterior cingulate as callosum something
> that was relevant just for the volume segmen
Hi Mike,
The midline fix for most updated version of Freesurfer (v4.0.0) does
indeed refer to the correction of the mislabelling of the rostral anterior
cingulate as the corpus callosum, which was present in the prior version.
Best,
rahul
>
> Hello,
> The Release Notes of v4.0.0 indi
may
be slightly painful if you have a large number of subjects) or use the
rostral middle frontal ROI, which encapsulates the DLPFC.
Hope this helps,
rahul
> Will Freesurfer allow me to measure ventromedial and dorsolateral
> frontal lobe volumes?
>
>
>
> Thanks,
>
&g
may
be slightly painful if you have a large number of subjects) or use the
rostral middle frontal ROI, which encapsulates the DLPFC.
Hope this helps,
rahul
> Will Freesurfer allow me to measure ventromedial and dorsolateral
> frontal lobe volumes?
>
>
>
> Thanks,
>
&g
.
follows the contours of sulcal boundaries) than the V3 image. There indeed
is some variablity between the V4 and V3 versions as the V4 version should
be more anatomically accurate than the prior version.
Hope this is of help,
rahul
> Hello,
>
> Is there any paper talking about the variabili
in
certain areas such as the anterior cingulate, entorhinal, and the inferior
parietal lobule. Where exactly do you find the most amount of difference
between the two versions?
Best,
rahul
> Hi Leila,
>
> do you see this in other subjects? We also have a utility
> (mris_divide_parce
Hi Xin,
For subcortical volumes, check the SUBJECT/aseg.stats file.
The thickness question I will leave for the Bruce, Doug and the others.
Best,
rahul
> Hello, Rahul
> Two more questions. 1. How can I get the volumes of subcortical
> structures, like in the presentation of f
Hi Hankee,
For the parahippocampal gyrus, I would do the following to correct for
head size:
Raw Parahippocampal volume (as derived from aparc.stats)/ICV (as derived
from aseg.stats)
Best,
rahul
> hi,
> Now I use the parahippocampal gyrus gray matter volume to divide the total
> gr
Hi Xin,
I will Doug handle this one. And please email the list in your replies.
Best,
rahul
On Mon, 30 Apr 2007, Wang, Xin wrote:
Many thanks, Rahul. I found readings in /stats/*h.aparc.stats. I am a freesurfer
beginner. I have another question. I want to compare the cortical thickness
and upload it into matlab, spss or any other stats package and do
statistics on these values.
Best,
rahul
On Mon, 30 Apr 2007, Wang, Xin wrote:
Dear Rahul
The SI is primary somatosensory cortex (or postcentral gyrus) and MI is primary
motor cortex (or precentral gyrus). I want to compare
Hi Xin,
What exactly do SI and MI cortices refer to?
rahul
On Mon, 30 Apr 2007, Wang, Xin wrote:
Hello, group
I need to compare thickness of left v.s. the right SI and MI cortices. I saw
some matlab tools for comparsion of left and right hippocampus in
Lundervold.pdf. I could not find
nd utilize these
as 'adjusted volume' measures for all further statistical comparisons.
Best,
rahul
> hi,rahul
> Sorry,I have not heard about the eTIV or ICV,what does this letter
> stand for? and how to use eTIV or ICV to adjust head size? Thank you
> very much!
>
recommendation would
be that if you are performing cross-sectional comparisons using the
volumes of individual brain regions, you should use the eTIV or ICV
measure to adjust for head size for individual subjects.
Best,
rahul
> hi,I have question about the ?h.aparc file in stats directory. Can I use
&g
(Parietal)
Best,
rahul
> Hi Bruce,
>
> Are you saying that you don't think I even could build these lobar groups
> using the existing codes in the LUT.txt file?
>
> Lee
>
> -Original Message-
> From: Bruce Fischl [mailto:[EMAIL PROTECTED]
> Sent: Saturday,
Hi Graham,
The insula has intentionally not been labeled in the parcellation atlas.
At the time the atlas was developed, we did not have a working definition
of the insula and thus in order to maintain the anatomic accuracy, decided
against making a label for it.
Best,
rahul
> Folks:
>
Hi Aaron,
In terms of purely anatomically, to calculate the total GM I would not
include the corpus callosum (a white matter structure) or the unknown
region (which is an amalgam of subcortical areas).
Best,
rahul
Hi, I wanted to calculate total surface-based cortical GM, and was
> wonder
Hi Nurunisa,
If you are using tksurfer to view the annotation files or an individual
label, you can first select the label you want to color code by clicking
on it. Then, you can bring the 'color spectrum' bar in tksurfer and choose
whichever color you would like.
Best,
Rahul
> Hi
Hi,
To add to what Bruce just mentioned, for visualization purposes, in
tksurfer under the View option bar, choose Label Style and select Outline.
This will allow you to visualize where the boundaries of each of the
regions of interest are.
Best,
Rahul
On Wed, 13 Dec 2006, Bruce Fischl
regards,
Rahul
Rahul S. Desikan
[EMAIL PROTECTED]
On Thu, 7 Dec 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Hi,
I have two questions:
1. I was wondering if the values of corpus callosum are useful
2. Why the values of the corpus callosum are included in the gray matter
data
Hi Dhruman,
Sorry, I meant 'occipital' not 'temporal' lobe.
rahul
On Thu, 27 Jul 2006, Rahul Desikan wrote:
Hi Dhruman,
If you are interested in lobe-wise comparisons, you can indeed add up the
individual regions of a specific lobe, create one massive label for
s you have
generated.
best,
Rahul
On Thu, 27 Jul 2006, Goradia, Dhruman D wrote:
Hi all,
I am interested in lobe wise surface measurement. I read Desikan et al.
paper to understand that their atlas divides the lobes into different
region and freesurfer uses that atlas to gets measurement for e
more
as an anatomic 'placeholder' for the cingulate regions than anything;
anatomically, in the parc. atlas this region is meaningless.
Hope that helps,
rahul
On Wed, 19 Jul 2006, Bruce Fischl wrote:
1) yes, I would do the surfaces.
2) ignore the WM volume in mris_anatomical_stats
bel Style-->choose Outline instead of Filled) to differentiate
cortical areas from non-cortical areas (i.e. corpus callosum, unknown).
best,
Rahul
On Tue, 20 Jun 2006, Jeffrey Spielberg wrote:
Hi, I had a couple of questions regarding cortical/subcortical segmentation-
1. In our co
i was using dev previously and got this error. then after the flurry of
emails yesterday switched to using stable (/usr/local/freesurfer/stable)
and got the same errors this morning.
thanks,
rahul
On Wed, 22 Mar 2006, Bruce Fischl wrote:
are you sure you're running stable, not d
Hi,
Has anyone noticed the previously reported problem with mri_ca_register in
the stable version? I have been using the stable version of the binaries
and have not been able to sucessfully generate asegs.
The script I use to generate the aseg.mgz file is:
/space/krupa/7/users/rahul/ppg
Hi Aaron,
Which version of Freesurfer and which version of the parc atlas are you
using? Also have you checked your surfaces along the midline to see if
they are acting in a strange way (i.e. self-intersecting, crossing the
midline, etc.)?
thanks,
Rahul
On Mon, 20 Mar 2006, Goldman, Aaron
Hi Greg,
Could you send along jpegs or rgbs detailing what excactly the
parcellation atlas is doing in the cingulate region? Also have you looked
at both the white and pial surfaces in this area?
Hope you are well othwerwise,
Rahul
On Sat, 18 Mar 2006, Greg Harris wrote:
Dear Karl,
Has
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