why I am asking.
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Monday, May 10, 2021 9:23 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] mris_anatomical_stats(
urfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to
surface
You can use mri_segstats on the output to get your table of values for each
ROI. Run it with --help and see example 5
On 4/27/2021 1:50 PM, Jensen, Alexandria wrote:
External Email - Use Cauti
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Fischl, Bruce
*Sent:* Monday, April 26, 2021 5:05 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] mris_anatomical_stats() for ODI maps
inflated to
Yes, I believe so depending on which parcellation you are using
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Nils B.
Sent: Thursday, April 29, 2021 9:55 AM
To: Freesurfer support list
Subject: [Freesurfer] mris_anatomical_stats
External Email - Use Caution
Dear
External Email - Use Caution
Dear Supportteam,
I have a short question concerning the data produced by
mris_anatomical_stats. The description on the anatomical structures is
really short so I just wanted to ask if the precentral stats are for the
precentral gyrus?
Best regards,
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to
surface
Oh, then you don’t need -l at all I don’t think. Have you sampled your ODI file
onto the surface?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Jensen, Alexandria
Sent: Monday, April 26
Oh, then you don't need -l at all I don't think. Have you sampled your ODI file
onto the surface?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Jensen, Alexandria
Sent: Monday, April 26, 2021 5:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_anatom
atlas.
Alexandria
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Fischl, Bruce
Sent: Monday, April 26, 2021 2:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to
surface
Hi Alexandria
April 25, 2021 8:35 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to
surface
what is your mris_anatomical_stats command and terminal o
/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
on behalf of Douglas N. Greve
Sent: Sunday, April 25, 2021 8:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_anatomical_stats() for ODI maps inflated to
surface
what is your mris_anatomical_stats command
what is your mris_anatomical_stats command and terminal output?
On 4/22/2021 4:48 PM, Jensen, Alexandria wrote:
External Email - Use Caution
Hello fellow Freesurfer users,
I am attempting to reproduce the analysis conducted by Parker et al.
in their 2018 paper, “Cortical microstr
External Email - Use Caution
Hello fellow Freesurfer users,
I am attempting to reproduce the analysis conducted by Parker et al. in their
2018 paper, “Cortical microstructure in young onset Alzheimer's disease using
neurite orientation dispersion and density imaging”
(https://s
r-boun...@nmr.mgh.harvard.edu>
on behalf of Douglas N. Greve
<mailto:dgr...@mgh.harvard.edu>
Sent: Wednesday, November 11, 2020 11:07 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer]
day, November 11, 2020 11:07 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] mris_anatomical_stats error: stating file
Can you send the exact command line that generated the terminal output
you sent? The line below has a different subject name. Run that
command from the shell (rather th
er-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Wednesday, November 11, 2020 11:07 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_anatomical_stats error: stating file
Can you send the exact command line that generated the terminal output you
sent? The line
Thank you for all your help!
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Thursday, November 5, 2020 9:44 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [
November 6, 2020 at 10:11 AM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] mris_anatomical_stats error: stating file
which version of FS are you using?
On 11/5/2020 11:29 AM, Chan, Shi Yu wrote:
Hi,
Yes, sorry! I copied the error message from terminal, but copied the com
* Thursday, November 5, 2020 9:44 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] mris_anatomical_stats error: stating file
Is that the right error msg? It says it can't find the RH, but you are
running it with LH. Can you post the entire terminal output?
On 11/3/202
ript I use in this email.
Thank you for all your help!
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Thursday, November 5, 2020 9:44 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_anatomical_stats erro
Is that the right error msg? It says it can't find the RH, but you are
running it with LH. Can you post the entire terminal output?
On 11/3/2020 2:00 PM, Chan, Shi Yu wrote:
Hi FreeSurferDevelopers,
I'm trying to calculate cortical thickness statistics from the Yeo 17
Network cortical pa
Hi FreeSurfer Developers,
I'm trying to calculate cortical thickness statistics from the Yeo 17 Network
cortical parcellation and have used mri_surf2surf to get the .annot files for
each subject.
However, when I run mris_anatomical_stats, I get an error:
ERROR: stating file
subjects_dir/sub-
Yes, that is the effect of including the cortex.label
On 8/31/20 8:28 AM, Palin, Tara wrote:
External Email - Use Caution
When using the following command line:
mris_anatomical_stats -th3 -mgz- cortex ../label/?h.cortex.label -f
../stats/?h.aparc.pial.stats -b -a ../label/?h.aparc.a
External Email - Use Caution
When using the following command line:
mris_anatomical_stats -th3 -mgz- cortex ../label/?h.cortex.label -f
../stats/?h.aparc.pial.stats -b -a ../label/?h.aparc.annot -c
../label/aparc.annot.ctab subject ?h pial
do we generate a pial surface area (
Hi Stephanie
specifying "pial" directs it to use the ?h.pial surfaces for e.g. surface
area measurement. What information are you hoping to extract from the
orig.mgz?
cheers
Bruce
On Thu, 17 Jan 2019, Winkelbeiner, Stephanie A wrote:
External Email - Use Caution
Hi Freesu
External Email - Use Caution
Hi Freesurfers,
I'm using the below command to extract GM values:
mris_anatomical_stats -mgz \
-cortex label/lh.cortex.label \
-f stats/lh.250.aparc.pial.stats \
-b -a 250.aparc \
-c label/colortable.ctab
not really. If you're running on a cluster, sometimes there can be
communication issues where it can only read part of a file, but that is
just a wild guess
On 10/13/17 12:44 PM, Keiko McCreary wrote:
Hi Doug!
I just ran the mris_anatomica_stats on its own- and it ran
successfully? Do you k
Hi Doug!
I just ran the mris_anatomica_stats on its own- and it ran successfully? Do
you know what may have caused it to fault?
Thank you very much!
Keiko
On Fri, Oct 13, 2017 at 12:17 PM, Douglas Greve
wrote:
> Does this happen repeatedly? You don't have to rerun recon-all again, just
> that
Does this happen repeatedly? You don't have to rerun recon-all again,
just that last mris_anatomical_stats command to see if it seg faults
again. If it does, first check your disk space, then load the left hemi
in freeview along with the annot and the cortex.label
On 10/13/17 11:05 AM, Keiko
what is this causing an error in?
On 08/29/2017 06:50 AM, Ernst Schwartz wrote:
> Hi!
>
> It seems that in FreeSurfer 6, the comma between “CortexVol” and
> “Total cortical gray matter volume” is missing
>
> here’s the relevant part of one of my stats-files:
>
> # Table of FreeSurfer cortical pa
Hi!
It seems that in FreeSurfer 6, the comma between “CortexVol” and “Total
cortical gray matter volume” is missing
here’s the relevant part of one of my stats-files:
# Table of FreeSurfer cortical parcellation anatomical statistics
#
# CreationTime 2017/08/23-20:19:44-GMT
# generating_progr
We do not output xls. You will have to convert it manually
On 08/18/2017 08:38 PM, std...@virgilio.it wrote:
> Hi list,
> how can I save the outputs of mris_anatomical_stats in xls file?
> Thanks
> Stefano
>
>
> ___
> Freesurfer mailing list
> Freesurfe
Hi list,how can I save the outputs of mris_anatomical_stats in xls file?Thanks
Stefano___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only
-b s71765 rh
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas Greve
Sent: Tuesday, June 13, 2017 1:52:58 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_anatomical_stats and cortical thickness
{Disarmed}
how did you d
harvard.edu/msg53380.html)
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas Greve
*Sent:* Friday, June 9, 2017 9:48:50 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] mris_anatomical_stats and cortical thickness
Have you
t: Friday, June 9, 2017 9:48:50 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_anatomical_stats and cortical thickness
Have you tried to view your label on the individual subject? If your original
analysis was on cortical thickness, then there will be a *ocn*.dat file in th
Have you tried to view your label on the individual subject? If your
original analysis was on cortical thickness, then there will be a
*ocn*.dat file in the output with the values for each input subject and
each cluster
On 6/6/17 10:14 AM, Taylor Hilton wrote:
Hi all,
I’m trying to extract
Sorry this didn’t seem to send the first time due to attachments most likely,
so I’ll leave them out and let me know if you need to look at them.
> On Jun 6, 2017, at 10:14 AM, Taylor Hilton wrote:
>
> Hi all,
>
> I’m trying to extract individual cortical thickness values using the output
> o
Hi Bruce,
Thank you so much for this suggestion.
In case anyone searches for this thread in the future, I am writing back to
report that it worked and thickness indices remain the same (although other
indices, which are of no interest to me for this analysis, did change).
Best,
Arkadiy
_
I think that would be ok, but an easy way to test it is to try it on
another subject first with their actual wm.mgz, then with the one from
fsaverage to check that the thickness is the same.
cheers
Bruce
On Sun, 11 Sep 2016,
Arkadiy Maksimovskiy wrote:
> Dear Freesurfer Experts,
>
> I am tryi
Dear Freesurfer Experts,
I am trying to run mris_anatomical_stats in order to extra thickness data
from my participants' label files. However, I only have access to a
subj_recon data (without wm.mgz in that folder).
Does anyone know if there is a way to extract the thickness measures for
every pa
Thanks! I will take your advice and start to learn it. I appreciate your
help so much!!
Elissa
On Tue, Mar 22, 2016 at 6:28 PM, Bruce Fischl
wrote:
> something like:
>
>
> set SUBJECTS = (subject1 subject2 ... subject60)
> foreach s ($SUBJECTS)
>foreach hemi (lh rh)
>mris_anatom
something like:
set SUBJECTS = (subject1 subject2 ... subject60)
foreach s ($SUBJECTS)
foreach hemi (lh rh)
mris_anatomical_stats -l $hemi.BA45.label $s $hemi
end
end
definitely worth taking the time to learn! It will save you endless amounts
of time in the longrun and it's
Thanks! I am a newbie so I think it would take me longer to learn how to
write the script then to just do it one at a time! :)
On Tue, Mar 22, 2016 at 6:23 PM, Bruce Fischl
wrote:
> oh, no, but write a script to do it! That's what unix is for.
>
> On Tue, 22 Mar
> 2016, Elissa Ash wrote:
>
> > T
oh, no, but write a script to do it! That's what unix is for.
On Tue, 22 Mar
2016, Elissa Ash wrote:
> Thanks Bruce
> I am calculating the thickness for a given ROI (rh.BA45.label) and comparing
> it
> across subjects and it is tedious to have to type in the command separately
> each time
> (~
Thanks Bruce
I am calculating the thickness for a given ROI (rh.BA45.label) and
comparing it across subjects and it is tedious to have to type in the
command separately each time (~60 subjects). I was hoping that there was a
way to input multiple subjects at once. That's it.
Thanks,
Elissa
On Tu
Hi Elissa
not really. What would you want it to do? There are tools for tabulating
the output of mris_anatomical_stats across subjects, if that's what you
are trying to do
cheers
Bruce
On Tue, 22 Mar 2016, Elissa Ash wrote:
>
> Dear experts,
>
> Is there any way to run the mris_anatomical_st
Dear experts,
Is there any way to run the mris_anatomical_stats command on more than one
subject at a time?
Thanks,
Elissa
--
Elissa Ash, MD, PhD
Director, Center for Memory and Attention Disorders
Department of Neurology
Tel Aviv Sourasky Medical Center
6 Weizmann St.
Tel Aviv 64239, Israel
97
>>
To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
Cc:
Date: Mon, 7 Mar 2016 18:50:01 -0500
Subject: Re: [Freesurfer] mris_anatomical_stats -th3
/*!
\fn MRISvolumeTH3(MRIS *w, MRIS *p, MRI *vol)
\brief Compute vertex-wise volume based on dividing each obli
To: freesurfer@nmr.mgh.harvard.edu
Cc:
Date: Mon, 7 Mar 2016 18:50:01 -0500
Subject: Re: [Freesurfer] mris_anatomical_stats -th3
/*!
\fn MRISvolumeTH3(MRIS *w, MRIS *p, MRI *vol)
\brief Compute vertex-wise volume based on dividing each obliquely
truncated
trilateral pyramid into three tetrahedra. Base
Dear Douglas,
I saw the previous tutorials didn't include this "-th3" flag, is there any
difference between the following two command lines?
mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c
../label/aparc.annot.ctab subje
/*!
\fn MRISvolumeTH3(MRIS *w, MRIS *p, MRI *vol)
\brief Compute vertex-wise volume based on dividing each obliquely
truncated
trilateral pyramid into three tetrahedra. Based on Anderson M. Winkler's
srf2vol matlab script.
\params w is white surface, p is pial. Output is an MRI stru
Dear guys,
I checked one of my subjects file /stats/lh.aparc.stats, in which it said
the commandline as:
mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c
../label/aparc.annot.ctab subject1 lh white
what does the flag "-t
hmmm, maybe upload the subject and we'll take a look?
On Wed, 15 Jul 2015,
O'Shea,Andrew wrote:
I tried loading the label and surfaces in free view and everything looks
normal to me. This is the output I get with mris info:
[aoshea@gator1 ~]$ mris_info
/scratch/lfs/aoshea/testAndrew/dotsonFSp
I tried loading the label and surfaces in free view and everything looks
normal to me. This is the output I get with mris info:
[aoshea@gator1 ~]$ mris_info
/scratch/lfs/aoshea/testAndrew/dotsonFSprocessed/EX03/surf/rh.white
SURFACE INFO
type: MRIS_
Hello all,
I am having an issue where the mris anatomical stats command is failing and
only printing 'segmentation fault' instead of the expected volume, area,
thickness, etc. This is happening for ~20% of the subjects, but seems to work
fine for the remaining 80%. All labels were created and ma
can you run mris_info on
/scratch/lfs/aoshea/testAndrew/dotsonFSprocessed//EX03/surf/rh.white
and/or view it in freeview to make sure it isn't corrupted?
On
Wed, 15 Jul 2015, O'Shea,Andrew wrote:
Hello all,
I am having an issue where the mris anatomical stats command is failing and
only prin
If you ran with -autorecon3, then you do not need to redo the labels. As
for the aseg, it depends on what you ran and what edits you made. If
you ran with -autorecon2 and you had added control points, then it
would change slightly.
You can ignore that matlab warning (it is only saying that yo
Hi Bruce,
Thank you!
Andreia
Quoting Bruce Fischl :
> Hi Andreia
>
> I haven't been following this whole thread, but the matlab warning is not
> a problem
>
> cheers
> Bruce
> On Tue, 20 May 2014, _andre...@sapo.pt wrote:
>
>> Hi,
>>
>> Do I need to run laleb2label and label2annot to get once
Hi Andreia
I haven't been following this whole thread, but the matlab warning is not
a problem
cheers
Bruce
On Tue, 20 May 2014, _andre...@sapo.pt wrote:
> Hi,
>
> Do I need to run laleb2label and label2annot to get once again the BA.thresh?
>
> Or is it enough to just extract the stats?
>
> I
Hi,
Do I need to run laleb2label and label2annot to get once again the BA.thresh?
Or is it enough to just extract the stats?
I already extracted the aseg stats and one of the subjects came out
with slightly different values this time, while the other presented
the same values. Was this suppo
Hi Marie,
Thanks for the input! Actually, from the recon-all log I can see that
autorecon3 was caled in the terminal, and comparing it to a subject
without any error they look the same to me. Also, qcache gave no error.
Anyway, I'll rerun -autorecon3 for these 2 subjects and all the
command
Hi Andreia,
Then I would guess that your error comes from the fact that you didn't rerun
the autorecon3 at that stage for these 2 subjects. As the randomness flag
changes the number of vertices when recreating the surfaces, that explains the
error. So for your subjects, just rerun autorecon3 (
BA.annot I think that was created before any problem because I had no
error (at least I didn't see any) untill I extracted aparcstats2table
of those values. But I just checked my notes and these two subjects
were the only ones that gave aberrantly high LGI values when running
-localGI. I t
On 05/19/2014 04:10 PM, _andre...@sapo.pt wrote:
>
> I just ran vno_match_check for all my subjects and the scenario is:
>
> *S_ubj1_*: mris_anatomical_stats -a BA.annot -t pial_lgi -f
> subj1/stats/lh.BA_lgi.stats subj1 lh
>
> the warning appears: *MRISreadAnnotationIntoArray*: vertex index out
If the subject is out of synch, then running mris_preproc or recon-all
-qcache should have failed too (as would have anything that tried to map
the subject to a group space). This usually happens when you make edits
to a subject but don't re-run the analysis all the way through (or the
analysi
I just ran vno_match_check for all my subjects and the scenario is:
S_UBJ1_: mris_anatomical_stats -a BA.annot -t pial_lgi -f
subj1/stats/lh.BA_lgi.stats subj1 lh
the warning appears: MRISREADANNOTATIONINTOARRAY: vertex index out of
range: 120389 i=0014C8B5, in_array_size=120388
ONLY FOR BRODM
Hi Doug,
That's really bad news. So I'll check all my subjects to track the
ones who give the error. Then I'll have to run each one from scratch?
I don't quite understand what went wrong with only a few subjects
since I did (as far as I'm aware) everything in the same way for all
of them. A
On 05/19/2014 02:32 PM, _andre...@sapo.pt wrote:
> Sorry for all the emails..
>
> Now I ran that same command on the second subject in which I only
> detected a problem for the left hemisphere when trying to get
> Destrieux lgi, and got this error but for both hemispheres:
>
> ERROR: subj2/surf/rh
Sorry for all the emails..
Now I ran that same command on the second subject in which I only
detected a problem for the left hemisphere when trying to get
Destrieux lgi, and got this error but for both hemispheres:
ERROR: subj2/surf/rh.orig has 121356 vertices, subj2/surf/rh.sphere
has 1213
Hi Doug,
I just ran that command on the first subject I referred and the output is:
> [user@localhost Freesurfer]$ vno_match_check subj lh
Checking subj/surf/lh.orig...
Checking subj/surf/lh.white...
Checking subj/surf/lh.pial...
Checking subj/surf/lh.inflated...
Checking subj/surf/lh.smoothwm...
Hello again,
Sorry for not waiting for your reply, but I realized that I get the
same warning with another different subject when trying to get
destrieux lgi and this happens only for the left hemisphere:
[user@localhost Freesurfer]# mris_anatomical_stats -a
aparc.a2009s.annot -t pial_lgi
I think it is still out of synch. Try running
vno_match_check subject lh
doug
On 05/16/2014 01:06 PM, _andre...@sapo.pt wrote:
> Hello,
>
> Only after sending the email below I noticed that now the stats file
> generated give only 0,00 were the LGI values should be, even though
> they appea
Hi Andreia,
You probably have lGI values that correspond to earlier versions of your
surfaces (I.e. maybe you ran lGI first, then did corrections on the surfaces
and reprocessed them, but forgot to recalculate lGI for this new surfaces).
If you simply reprocess lGI now, that should solve the p
Hello,
Only after sending the email below I noticed that now the stats file
generated give only 0,00 were the LGI values should be, even though
they appear in the terminal.
How can I solve this issue? And, again, are all the measures (cortical
thickness, surface area, aseg) invalidated? As
Hi Doug,
I tried to load the annotation and it gave an error. I look in the
archives and I found someone with the same problem and the advice was
to run:
recon-all -s -sd -make all
I did that and tried to run again mris_anatomical_stats as previously
and still have this warning
subj/st
That probably means that the subject is out of synch. Try viewing the
subject's surface tksurfer or freeview and load the annotation.
doug
On 05/14/2014 10:25 AM, _andre...@sapo.pt wrote:
>
> Hello all,
>
> I generated the lgi.stats file for all my subjects and in one of them
> I got this warni
Hello all,
I generated the lgi.stats file for all my subjects and in one of them I
got this warning:
mris_anatomical_stats -a aparc.annot -t pial_lgi -f
SUBJ/stats/lh.aparc_lgi.stats SUBJ lh
computing statistics for each annotation in aparc.annot.
using thickness file pial_lgi.
reading volu
Hi Louis,
It didn't work either. This is what shows up in the terminal after
running mris_anatomical_stats:
mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a
./rh.aparc.annot -c ./aparc.ctab FERNANDORODRIGUES rh pial
INFO: assuming MGZ format for volumes.
computing statistics for eac
Hi Andreia,
If you remove the underscore from aparc_pial for the --parc flag in the
aparcstats2table command, that should do the trick.
-Louis
On Wed, 26 Mar 2014, _andre...@sapo.pt wrote:
> Hello list,
>
> I'm trying to get aparc surface area from the pial surface in a table
> using aparcstats2
Hello list,
I'm trying to get aparc surface area from the pial surface in a table
using aparcstats2table but I'm not being able to...
I've already created the file aparc_pial.stats inside the stats dir
running the following command line from the subjects's label dir:
mris_anatomical_stats -m
Hi Krista
the optional last argument for mris_anatomical_stats is a surface name
(not a scalar field over the surface, like the thickness file)
cheers
Bruce
On Mon, 9 Dec 2013, krista kelly wrote:
Hi,
I'm trying to run mris_anatomical_stats to get cortical thickness from
labels for each p
Hi,
I'm trying to run mris_anatomical_stats to get cortical thickness from
labels for each participant but I keep getting the following error:
MRISread: file '/Applications/freesurfer/subjects/MB19/surf/lh.thickness'
has many more faces than vertices!
Probably trying to use a scalar data file as
If you have 5.3, you run
recon-all -s subject -cortparc -parcstats
will update just the aparc annotation and the corresponding stats files
doug
On 9/17/13 4:49 PM, Gomar, Jesus wrote:
Dear Freesurfer experts,
I hope someone can help me with a couple of questions regarding the
use of mris
Dear Freesurfer experts,
I hope someone can help me with a couple of questions regarding the use of
mris_anatomical_stats command:
1. I am using mris_anatomical_stats to compute perirhinal thickness but with
subjects I had previously recon through v5.1.0, and of course the
mris_anatomical_sta
Hi Li,
there you go,
Gari
https://docs.google.com/open?id=0Byf71TWfovledFhJYWN2cGtHV00
On 2012-09-15, at 19:38, "Kong, Li" wrote:
> Hi Gari,
> I saw your email to Alex about your method obtaining statistics from multiple
> subjects with Python script. Could you send the code to me?
>
> Th
Hi Alex,
I am using the same method, I created a Python script to automate it for
multiple users.
Basically, if you give it a file with all the subject ID-s, it maps labels with
mri_label2label, obtains statistics with mris_anatomical_stats and writes all
the stats in a single file.
You also
Hi again,
This is a follow-up question to my previous email -- the method I used may
not be the most efficient or the correct way to extract cortical thickness
from manually created ROIs. I'm unfamiliar with how to obtain thickness
data from a label, so I'm not sure if what I did is correct or if
Hi Doug and Freesurfers,
I'm currently working on extracting thickness measurements from an ROI I
manually created. I created my ROI label in tksurfer and applied the label
to each subject I'd like to extract thickness data from using
mri_label2label. I then used the following command to generate
Hi Doug
Yes, this is exactly what I looked for.
Thanks a lot
Cheers
Jürgen
On [DATE], "Douglas N Greve" <[ADDRESS]> wrote:
> Hi Juegen, there will be a file called something like
> cache.th20.abs.y.ocn.dat in the glm output directory. This will be a
> text file with number of columns equal to
Hi Juegen, there will be a file called something like
cache.th20.abs.y.ocn.dat in the glm output directory. This will be a
text file with number of columns equal to the number of significant
clusters (after correction) and number of rows equal to the number of
subjects. The value will be the av
Hi Doug
I correlated a behavioural measure with cortical thickness and surface area
using mri_preroc, mri_surf2surf and mri_glmfit. Now I would like to extract
the individual values of the clusters that correlated with the behavioural
measure.
Because the individual values should be comparable wi
Use "--sval lh.area". Also, why do you want to smooth it before
averaging over the ROI?
doug
On 06/07/2012 01:29 AM, Jürgen Hänggi wrote:
> Hi Doug
>
> This is my command line:
>
> mris_anatomical_stats -a area_left_significant_labels.annot -t lh.area
> -nsmooth 15 -f $s/stats/lh.aparc.a2005s.sta
Hi Doug
This is my command line:
mris_anatomical_stats -a area_left_significant_labels.annot -t lh.area
-nsmooth 15 -f $s/stats/lh.aparc.a2005s.stats $s lh
In the past, you recommended smoothing the data with mri_surf2surf instead
of with mris_anatomical_stats.
For that purpose, I run the follo
what is your command line?
doug
On 6/6/12 5:25 AM, Jürgen Hänggi wrote:
> Dear FS experts
>
> I have done group comparisons wrt thickness and surface area. The
> found clusters were written out as annotations, transformed into each
> individual space, and then the corresponding values were extract
Dear FS experts
I have done group comparisons wrt thickness and surface area. The
found clusters were written out as annotations, transformed into each
individual space, and then the corresponding values were extracted.
When using mris_anatomical_stats, values are different for thickness maps
dep
Dear FS experts
I have done group comparisons wrt thickness, surface area and volume. The
found clusters were written out as annotations, transformed into each
individual space, and then the corresponding values were extracted.
When using mris_anatomical_stats, values are different for thickness
Jurgen,
Both of these files were created with identical command lines.
doug
Jürgen Hänggi wrote:
> Hi Doug
>
> Attached are the two files generated from the same subject by using
> mris_anatomical_stats, once without smoothing (rh.aparc.a2005s.stats) and
> once with smoothing (rh.aparc.a2005s_wit
Juegen, can you send the full terminal output? Also, you can try
explicitly smoothing the file with mri_surf2surf and then run anatomical
stats on the smoothed file.
doug
Jürgen Hänggi wrote:
> Dear FS experts
>
> I tried to read out in each subject the surface area values of some clusters
> der
Dear FS experts
I tried to read out in each subject the surface area values of some clusters
derived from a group comparison.
For that purpose, I used mri_surf2surf and mris_anatomical_stats.
Everything worked fine, but in some clusters the direction of the effects
reversed. A first guess was tha
Dear FS experts
I tried to read out in each subject the surface area values of some clusters
derived from a group comparison.
For that purpose, I used mri_surf2surf and mris_anatomical_stats.
Everything worked fine, but in some clusters the direction of the effects
reversed. A first guess was tha
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