Hi,
Will it be possible to incorporate the new hippo subfields atlas and stats
generation in the 5.3 recon-all without having to process everything from
scratch with 6.0?
Thank you,
Andreia
Citando Eugenio Iglesias :
Dear Erik / Angela,
the atlas in 5.3 was derived from manual annotations on
Ok. Then, I'm not sure if everything is correct with the command lines
since I use 5.0.
Any thought on this Freesurfer team?
Thanks,
Andreia
Citando will brown :
Thanks again, for the record, I'm using freesurfer version 5.3.0 on
Centos 6.
On 9/09/2014 11:00 PM, <_andre...@sapo.pt> wrote:
Hi Will,
Just to clarify, what version of FS are you using? I think it might not be
5.0 and I don't know if everything aplies if we are using different
versions.
1) Yes, it is only based on the pial surface (and these command lines are
for the aparc, DK altas). The second set provides the surfac
Hi Will,
I use the following commands to get surface area from the pial surface:
In the subject label dir:
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.APARC.PIAL.stats -b -a ../label/lh.aparc.annot -c
../label/aparc.annot.ctab SUBJ lh pial
mris_anatomical_stats
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,
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
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
from scratch or is there any other solution?
Thank you,
Andreia
Quoting Douglas N Greve :
On 05/19/2014 02:32 PM, _andreia_@sapo.ptwrote:
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 ge
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
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 -
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
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
- Mensagem encaminhada de _andre...@sapo.pt -
Data: Mon, 31 Mar 2014 14:45:00 +0100
Hello!
I'm reposting my email without attachments this time since it is not
getting to the list if I have attachments.
Could you advice please?
Thank,
Andreia
- Mensagem encaminhada de _an
I cannot properly access my desktop PC today, tomorrow I'll give you
feedback, However, with a corase inspection the surfaces look ok.
Thank you Bruce!
Andreia
Quoting Bruce Fischl :
> the easiest way is to just use the aparc+aseg.mgz
>
> cheers
> Bruce
> On Sun, 30 Mar 2014,
> _andre...@sa
How do I overlay aparc labels in tkmedit? I can load Brodmann area
labels, but not aparc.
Thanks!
Andreia
Quoting Bruce Fischl :
> and what do the surfaces look like in those regions? For the wm surface
> are to be larger it probably needs to be a lot less smooth
>
> On Sun, 30 Mar 2014, _and
Hi,
Sorry, I mixed it up in text of the first email. The WM is bigger. The
values of the example are correct.
Thanks!
Quoting Bruce Fischl :
> Hi Andreia,
>
> which one is bigger? In your first email you said pial (which should be)
> and in your second you said white matter
>
> cheers
> Bruc
Hello,
What could be the reason to get bigger surface area from WM surface
than from the pial surface in the 3 labels?
Thank you!
Andreia
- Mensagem encaminhada de _andre...@sapo.pt -
Data: Fri, 28 Mar 2014 17:43:43 +
De: _andre...@sapo.pt
Assunto: Re: [Freesurfer] Fwd:
Hi Doug,
Thank you very much! It did the trick!
However, I've noticed that the surface area obtained from the pial
surface is bigger than the one obtained from white surface in 3 labels:
Example of a control subject:Bankssts(WM=1161; pial=1026),
pericalcarine(WM=1614, pial=1412) and insula(W
Hello all,
How do I get aparc stats (area) using the pial surface, please?
Thanks,
Andreia
- Mensagem encaminhada de _andre...@sapo.pt -
Data: Thu, 27 Mar 2014 11:31:13 +
De: _andre...@sapo.pt
Responder Para: Freesurfer support list
Assunto: Re: [Fr
Hi Doug,
I had to "Save file as"... So, that was the download... Backup made
and mris_preproc replaced by the new one.
Thank you!
Andreia
Quoting Douglas N Greve :
> download the file and copy it into $FREESURFER_HOME/bin and make it
> executable (make a backup first)
>
>
> On 03/27/2014 09
Hello list,
I'm working with FS 5.0 and I'll be using either qdec or mri_glmfit
for whole brain analysis.
The link
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi#Installation
takes me to
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/mris_preproc
where a script appears. I th
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
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
I was also referring to the surface area and thickness (looking at the
files originated from white matter, which is also the default for
aparc I think):
For surface area
aparc= 72998.7
total= 72999
cortex=78090
For CT
aparc= 2.422
total= 2.422
cortex= 2.313
And also, which volume measure
Hello list,
I have a question regarding what stats are more correct to use to get
whole hemisphere surface area and mean thickness.
The cortex.label values extracted using the two bottom command lines
don't match aparc stats, however they match in the number of vertices
between them, and us
My apologies Doug... I thought that this email had all the history...
Narly, sorry for "invading" your discussion...
My questions came from the first email of Narly which referred to the
bug in mris_preproc:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg19821.html
This bug
Hi all,
just two quick questions: to what FS version is this related? And what
is wrong to do if one does not have the fix? Using what
stats/procedures?
Thanks,
Andreia
Quoting Douglas N Greve :
>>> why would one control for total brain volume in doing vertex-based
> analyses when the vertex-b
Hi all,
just two quick questions: to what FS version is this related? And what
is wrong to do if one does not have the fix? Using what
stats/procedures?
Thanks,
Andreia
Quoting Douglas N Greve :
>>> why would one control for total brain volume in doing vertex-based
> analyses when the vert
Hi Doug,
Thank you very much! It's working!
Andreia
Quoting Douglas N Greve :
> Not sure. Try running it with --nohash. It will probably take a lot longer
> doug
>
>
> On 03/12/2014 02:45 PM, _andre...@sapo.pt wrote:
>>
>> Hello list,
>>
>> When running the following command :
>>
>> mri_label2
Hello list,
When running the following command :
mri_label2label --srcsubject fsaverage --srclabel
/home/user/visao/Freesurfer/fsaverage/label/lh.BA1.thresh.label
--trgsubject subjid --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod
surface
I get the error
"INFO: found 1014 nlabel po
Dear list,
To obtain the thickness, surface area and volume values for each
hemisphere I ran the command line in the subjdir:
mris_anatomical_stats -mgz -f ../stats/lh.cortex_white.stats subjid lh white
And did that with the pial surface too. However, the values I get from
the generated cort
Hi Doug,
I would like to have the thickness map restricted to the BAs where the
group differences showed up. Could it be possible to overlay the
thickness map of an individual and then restrict it to the chosen BA,
for example?
The ideia is to have two subjects with the thickness overlayed
Hello list!
Is there a way to display the thickness of individual Bordmann areas
in the inflated surface using tksurfer?
I'm able to show surface area with File-> Label -> Load label and
choosing the thresholded label. Now, I qould like to do the same but
with cortical thickness, is this p
Hi Bruce,
I did that test some time ago (each sequence alone or averaged) but
only with one control subject. I then checked the values of different
measures and the cortical thickness maps for each situation and they
were very similar indeed. I did it only with one subject because the
poin
Hello list,
I have a group of subjects (4 patients and 8 controls) in which one
MPRAGE sequence was used and another group of subjects (2 patients and
2 controls) where a diffent MPRAGE was used. Both groups were acquired
in the same scanner. For each subject I have two anatomical sequences
I'll bear that in mind next time!
Thank you!!
Andreia
Quoting Anastasia Yendiki :
> No problem, you can usually find the answers to most of these types
> of questions in the help text of the commands. For example if you
> run "mris_label2annot --help" you'll see:
>
> [...]
>
> --a annotname
It was automatically created in the same folder of the old one -> label
However, inside this folder there are the old rh.BAxxx.label. The new
ones (BAxxx.thresh.label) were created inside the Freesurfer folder,
could it be related to that?
Quoting Anastasia Yendiki :
> What's the location
After running the mri_label2label and mris_label2annot a new
rh.BA.annot file was created (I had to remove the old one since it
doesn't overwritte) but when running
[user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f
../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab SUBJECT rh white
Nevermind the last email... If I change the output (wich is the second
place where BAxx.label appears, right?) file name and give the subjs
id this won't be a problem... Anyway, what are these files for? Will I
need to use them somehow?
Thanks
Andreia
Quoting _andre...@sapo.pt:
> Addicion
Hi,
I run the command for each BA labels of the right hemisphere and then run:
[user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f
../stats/rh.BA.thresh.stats -b -a ./rh.BA.annot -c ./BA.ctab SUBJECT
rh white
Which resulted in:
INFO: assuming MGZ format for volumes.
computing statistics
Ok. So the first is the input and the second is the output, correct?
So I'll have a different file for each out put? Is it possible to have
a table with the different measures after the threshold?
Thank you very much and I apologize for the naive questions...
Andreia
Quoting Anastasia Yendi
Ah ok! Sorry... In both places?
Quoting Anastasia Yendiki :
> It's .thresh.label, not .threshold.label.
>
> On Mon, 25 Mar 2013, _andre...@sapo.pt wrote:
>
>>
>> Hi Anastasia!
>>
>> The command in the recon-all.log is this one:
>>
>> mri_label2label --srcsubject fsaverage --srclabel
>> /home/u
Hi Anastasia!
The command in the recon-all.log is this one:
mri_label2label --srcsubject fsaverage --srclabel
/home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label --trgsubject
SUSANAFERREIRA --trglabel ./rh.BA1.label --hemi rh --regmethod surface
And I tried substituing BAxxx.label by BA
Hello list!
Any suggestions on what I may be doing wrong?
Thanks!
Andreia
- Mensagem encaminhada de _andre...@sapo.pt -
Data: Sun, 24 Mar 2013 19:11:13 +
De: _andre...@sapo.pt
Assunto: Re: [Freesurfer] Brodmann area thickness, surface area and volume
Para: Anastasia Y
Hi all,
I want to study Brodmann Areas cortical thickness, surface area and
volume. I've added the 5.2 BAxxx.threshold.label to my 5.0 fsaverage
and run the recon-all BA labels command. Now I run aparcstats2table
and get a table with the values but they are the same as before
running the B
Ok, that was my guess... I am running against a deadline, any news on
automatically computing the correct threshold script? Will I be able
to use it in 5.0?
Thanks you!
Andreia
Quoting Bruce Fischl :
> yes. Surface area will be the affected much more than thickness (and
> volume of cours
Hello!
After completing the talairach correction in tkregister2 (saving the
changes with the SAVEREG button), I am running recon-all -all -s subj.
But now I'm wondering if by doing it this way the changes will be
incorporated or the process will start from the beggining leaving
everything
Hi Bruce,
Thank you for the quick response!
In the meanwhile, does that also apply to cortical thickness and volume?
Thank you!
Andreia
Quoting Bruce Fischl :
> Hi Andreia
>
> the issue is that the BA labels contain every point that has any non-zero
> probability (no matter how small!) of bei
Hi all,
I'm using FS 5.0 and some time ago I was told by Bruce that I had to
threshold the BA in order to have an approximate area when overlaying
in the inflated surface. To get surface area values I also need to use
the label_area and put a threshold
having the possibility to choose the su
Hi!
I'm reposting my question:
Is there a command line to obtain the BA values with the recommended
thresholds (e.g. 0.9 for V1) from all subjects at once? At least for
each area at once for all subjects?
Thank you,
Andreia Pereira
___
Freesurf
Hi!
Is there a command line to obtain the BA values with the recommended
thresholds from all subjects at once?
Thank you,
Andreia Pereira
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fre
Thanks Bruce! Those are the main questions now (not only to V1, but
also to the rest of the Brodmann areas). I really want to be sure
where the measures come from. I want that the different measures (i.e.
cortical thickness and area are really from the same region in the
cortex), to know wh
Hi Bruce,
I'm using freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0.
I will also be using FS 5.1 paralelly.
Thank you very much!!
Andreia
Citando Bruce Fischl :
> Hi Andreia
>
> I just modified label_area to allow the specification of a threshold
> (with -t ) and a surface (with -s ), and
(sorry, here it is for the list again)
- Mensagem encaminhada de Bruce Fischl -
Data: Mon, 23 Apr 2012 15:30:17 -0400 (EDT)
De: Bruce Fischl
Assunto: Re: [Freesurfer] Load Brodmann surface area into inflated surface
Para: _andre...@sapo.pt
Hi Andreia,
can you cc the lis
(forgot to do answer all, here it goes for the list too)
Citando _andre...@sapo.pt:
> Hi Bruce,
>
> The ideia is to show one control subject vs. one patient inflated
> surface with BA surface (not volume, sorry) to show the difference
> (reduced surface area in one patient). Loading the rele
Hi all,
I'm sorry if these questions have already been covered here, but I've
looked into the archives and still can't do what I need (and since I'm
running out of time for this task I decided to post here):
I'm using version 5.0.0.
I want to show the resulting Brodmann area (only 3 BA) volu
Since it is such a straightforward correction, I've been making it
because I thought that it would have some effect (though tiny).
Thanks!
Andreia
Citando Bruce Fischl :
> yes, exactly. it will have a tiny effect on total surface area, but
> that includes noncortical regions anyway
> On Thu,
Ah ok! :)
So it won't affect any stats?
Anyway, not correcting this will make the inflated surface to have a
prominence, right? In that case it will only look better for results'
displaying.
Andreia
Citando Bruce Fischl :
> if they are coincident then it is accurately detected as
> non-
Hi Julia,
I usually remove the voxels from brainmaks.mgz for the pial edits but also
from wm.mgz. If you deselect the button of the pial surface in tkmedit, you
will see that the white matter surface is coincident with the pial, so you
also need to correct that volume. With wm.mgz as auxi
Hello!
I'm moving to FS 5.1 and I will be analysing retinotipic data (and the
anatomical data bas well). I would like to know if there are any
changes or issues while running this analysis in this new version
before I move.
Thanks,
Andreia
___
Fre
Hi everyone,
I'm sorry to bring this question up again, but I'm thinking to install
version 5.1 in the same computer where version 5.0 is installed.
However I'm thinking of installing the new one in another user account
that I've created only for this porpuse. My question is, can I install
Hi everyone,
I'm sorry to bring this question up again, but I'm thinking to install
version 5.1 in the same computer where version 5.0 is installed.
However I'm thinking of installing the new one in another user account
that I've created only for this porpuse. My question is, can I install
Hi!
Ok! That would be a good improvement :)
Thanks to both!
Cheers,
Andreia
Citando Douglas N Greve :
> Actually, you are right! Most of the non-gray matter structures in the
> medial wall are zeroed out, but the part that goes through the hippo and
> amygdala are non-zero. As Mike points
Hello,
Recalling these emails:
"The methods are somewhat different. For the value in the aseg.stats
table, the method is to compute the total volume inside the pial surface
and subtract the total volume inside the white surface. For
mris_anatomical_stats, the method is to compute the thickness ti
Thanks! I'll try that!
Andreia
Citando Nick Schmansky :
> you can try:
>
> -talairach -use-mritotal
>
> which will use an alternate talarairch alignment scheme (from the MNI).
> it sometimes works better.
>
> you should also probably add:
>
> -nuintensitycor-3T
>
> to the end of your recon-al
Hi all,
I have the same problem. I'm also working with 3T, and I need to
stretch the movable template with tkregister2 in almost every subject.
It would be nice if this wasn't necessary, is there a workaround?
Thanks,
Andreia
Citando Maria Felber :
> Dear Ms. Kakunoori,
>
> sorry to bother
Thanks Bruce and Douglas!
Andreia
Citando Douglas N Greve :
> mri_compute_volume_fractions will compute the fractions for each of
> the tissue types, no need to alter the segmentations.
> doug
>
>
>
> Bruce Fischl wrote:
>> Hi Andreia
>>
>> you could certainly change our segmentation labels
Hello list,
Following this email that I found in the archives:
"(...)
For the segmentation, FS still works voxelwise, but it's objective is
to identify each structure as a whole, whereas SPM and FSL/FAST
attempt to classify each voxel as being GM, WM or CSF. A short
description of the meth
Hello all!
I got no answer on this email, thus I'm posting these questions again,
hoe someone can help:
Hello!
About synthesising a volume using mri_volsynth with direction cosines
and RAS from mrs header:
In the mrs header I have:
- VOI position in the 3 views (sag, cor and tra) which are
FreeSurfers,
Is there a way to get BA cortical thickness in a table to export from
FS? As there is for aseg and aparc stats.
Thanks!
Andreia
--
Andreia Pereira, MSc student
Visual Neuroscience Laboratory
IBILI-Faculdade de Medicina
Azinhaga de Santa Comba
3000-354 Coimbra Portugal
Phone +(3
Hi,
I'm not being able to solve the segmentation problem on in this
subject. What files do I need to upload and were, please?
Thank you,
Andreia
Citando Bruce Fischl :
> Hi Andreia
>
> it's tough to tell from one slice. There appear to be some bright stuff
> in the superficial gray matter, w
Hello!
About synthesising a volume using mri_volsynth with direction cosines
and RAS from mrs header:
In the mrs header I have:
- VOI position in the 3 views (sag, cor and tra) which are from the
left upper corner of the voxel (these are the RAS coordinates that I
need to feed into mri_vols
Hi Doug,
Ok. Thank you! :)
Andreia
Citando Douglas N Greve :
> Yes, that should work. You will need a registration matrix to give to
> mri_compute_volume_fractions. You can get this from tkregister2:
>
> tkregister2 --mov mrs.vol.nii --s subject --regheader --reg register.dat
>
> when you run t
Dear list,
I am performing single-voxel and multivoxel spectroscopy analysis and I need to
do partial volume correction. I found a thread on the list of someone asking if
it possible to achieve this using Freesurfer (see below), but there is no
answer saying how it is done. My question is how c
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