Hi Bruce, I was running multiple recon-all scripts at the same time. Let me try
a fresh run on that subject to see if that's the issue. If I get another error,
I will write back.
********************************************
Michael Amlung, Ph.D.
Assistant Professor
Department of Psychiatry and Behavioural Neurosciences
DeGroote School of Medicine
McMaster University
Peter Boris Centre for Addictions Research
100 West 5th Street
Hamilton, Ontario L8N 3K7
Canada
Telephone: (+1) 905-522-1155, ext. 39014
Email: amlu...@mcmaster.ca
Web: http://fhs.mcmaster.ca/psychiatryneuroscience/AmlungMichael.html
-----Original Message-----
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of
freesurfer-requ...@nmr.mgh.harvard.edu
Sent: Wednesday, September 09, 2015 12:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 139, Issue 14
Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
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You can reach the person managing the list at
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When replying, please edit your Subject line so it is more specific than "Re:
Contents of Freesurfer digest..."
Today's Topics:
1. Re: Creating label from Tal coordinates
(Rodriguez-Thompson, Anais)
2. Re: Creating label from Tal coordinates (Douglas N Greve)
3. Re: mri_glmfit-sim error (Douglas N Greve)
4. Re: conjunction map (Douglas N Greve)
5. Re: mri_glmfit-sim error (Xiaomin Yue)
6. Functional connectivity with volume label
(Rodriguez-Thompson, Anais)
7. Automaticky: Jan Sanda is out of the office (a vr?t? se ne
13.9.2015) (jan.sa...@fnmotol.cz)
8. Re: mri_compute_volume_fractions not filling some sulci
properly (Bruce Fischl)
9. Help with recon-all (Amlung, Michael)
10. Re: mri_compute_volume_fractions not filling some sulci
properly (Bruce Fischl)
11. Re: Help with recon-all (Bruce Fischl)
12. TrackVis Transforms (Thomas Potrusil)
13. Re: TrackVis Transforms (Anastasia Yendiki)
14. Freesurfer/Qdec brain images (Lim, Lena)
----------------------------------------------------------------------
Message: 1
Date: Tue, 8 Sep 2015 20:27:10 +0000
From: "Rodriguez-Thompson, Anais"
<arodriguez-thomp...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Creating label from Tal coordinates
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<2d9198b56d6d9a41942f94ef7248a74f05229...@phsx10mb19.partners.org>
Content-Type: text/plain; charset="us-ascii"
Hi Doug,
I didn't see a colored dot. Unlike tksurfer, I didn't see a fill option to create a label
from a point. Is there something I should do other than moving the cursor to my point of
interest and then "save label as?"
Thanks,
Anais
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, September 08, 2015 2:47 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Creating label from Tal coordinates
There are no points in the label. I'm not sure that you actually created a
label. Did you have tkmedit configured to draw labels? Actually, I think it
open that way... Did you see a colored dot where your label was?
On 09/08/2015 02:04 PM, Rodriguez-Thompson, Anais wrote:
Hi Freesurfer experts,
I am trying to create a label from Talairach coordinates. I loaded the fsaverage brain in tkmedit
(tkmedit fsaverage orig.mgz) and entered the coordinates 0 -16 -6 (our coordinates of interest).
From here I saved the label using "save label as". However, when I try to load this
label, I get the error "tkmedit couldn't read the label you specified. This could be because
the format wasn't valid or the file wasn't found."
The actual label file reads:
#!ascii label
/cluster/roffman/users/Stable5_PerRun/fsaverage1/label/vta , from
subject fsaverage vox2ras=TkReg
0
Do you know why I'm having trouble making/visualizing a label created from Tal
coordinates and how I can do so?
Thanks,
Anais
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 2
Date: Tue, 08 Sep 2015 16:59:35 -0400
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Creating label from Tal coordinates
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <55ef4c37.1050...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
use the middle mouse button to create the label, then save it
On 09/08/2015 04:27 PM, Rodriguez-Thompson, Anais wrote:
Hi Doug,
I didn't see a colored dot. Unlike tksurfer, I didn't see a fill option to create a label
from a point. Is there something I should do other than moving the cursor to my point of
interest and then "save label as?"
Thanks,
Anais
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, September 08, 2015 2:47 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Creating label from Tal coordinates
There are no points in the label. I'm not sure that you actually
created a label. Did you have tkmedit configured to draw labels?
Actually, I think it open that way... Did you see a colored dot where your
label was?
On 09/08/2015 02:04 PM, Rodriguez-Thompson, Anais wrote:
Hi Freesurfer experts,
I am trying to create a label from Talairach coordinates. I loaded the fsaverage brain in tkmedit
(tkmedit fsaverage orig.mgz) and entered the coordinates 0 -16 -6 (our coordinates of interest).
From here I saved the label using "save label as". However, when I try to load this
label, I get the error "tkmedit couldn't read the label you specified. This could be because
the format wasn't valid or the file wasn't found."
The actual label file reads:
#!ascii label
/cluster/roffman/users/Stable5_PerRun/fsaverage1/label/vta , from
subject fsaverage vox2ras=TkReg
0
Do you know why I'm having trouble making/visualizing a label created from Tal
coordinates and how I can do so?
Thanks,
Anais
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
------------------------------
Message: 3
Date: Tue, 08 Sep 2015 17:03:23 -0400
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_glmfit-sim error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <55ef4d1b.7040...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
Use "abs" not "<abs>"
On 09/04/2015 03:20 PM, Xiaomin Yue wrote:
Hi,
I got this error when run mri_glmfit-sim: missing name for redirect.
I am running freesurfer 5.3. the command is: mri_glmfit --glmdir
ces.nii --cache 2 --sim-sign <abs>. The ces.nii was generated from
group level analysis (isxconcat-sess).
Thanks for your help.
Xiaomin
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
------------------------------
Message: 4
Date: Tue, 08 Sep 2015 17:03:58 -0400
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] conjunction map
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <55ef4d3e.3090...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
no, use mri_concat with the --conjunct option
On 09/04/2015 12:08 PM, std...@virgilio.it wrote:
Hi list,
is possible to obtained a conjunction map from vlrmerge command on
FS-FAST (resting state) results?
Stefano
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
------------------------------
Message: 5
Date: Tue, 8 Sep 2015 21:34:34 +0000
From: Xiaomin Yue <yu...@hotmail.com>
Subject: Re: [Freesurfer] mri_glmfit-sim error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <blu406-eas14916d41207a9074635a75bb3...@phx.gbl>
Content-Type: text/plain; charset="utf-8"
Thanks
Xiaomin
On Tue, Sep 8, 2015 at 2:03 PM -0700, "Douglas N Greve"
<gr...@nmr.mgh.harvard.edu> wrote:
Use "abs" not "<abs>"
On 09/04/2015 03:20 PM, Xiaomin Yue wrote:
Hi,
I got this error when run mri_glmfit-sim: missing name for redirect.
I am running freesurfer 5.3. the command is: mri_glmfit --glmdir
ces.nii --cache 2 --sim-sign <abs>. The ces.nii was generated from
group level analysis (isxconcat-sess).
Thanks for your help.
Xiaomin
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
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 for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
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------------------------------
Message: 6
Date: Tue, 8 Sep 2015 22:42:09 +0000
From: "Rodriguez-Thompson, Anais"
<arodriguez-thomp...@mgh.harvard.edu>
Subject: [Freesurfer] Functional connectivity with volume label
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<2d9198b56d6d9a41942f94ef7248a74f05229...@phsx10mb19.partners.org>
Content-Type: text/plain; charset="us-ascii"
Hi Freesurfer experts,
I'm trying to run a functional connectivity analysis using a label that was
created in the volume (vta.label). I have a few questions about how I would do
this (compared to a label created on surface).
Usually, we create a smoothed mask using the commands
mri_label2label --s fsaverage --regmethod surface --hemi {hemi} --srclabel
$SUBJECTS_DIR/fsaverage1/label/{label}.label --trglabel
$SUBJECTS_DIR/fsaverage1/label/junk.label --outmask
/cluster/roffman/users/Stable5_PerRun/fsaverage1/mri/{label}_sm00_bin.mgh
mris_fwhm --i
/cluster/roffman/users/Stable5_PerRun/fsaverage1/mri/{label}_sm00_bin.mgh
--fwhm 4 --smooth-only --o
/cluster/roffman/users/Stable5_PerRun/fsaverage1/mri/{label}_sm04.mgh --s
fsaverage --hemi rh end
I tried running mri_label2label using --regmethod volume, but the command window says
"ERROR: cannot specify outmask with vol reg method"
Do you know how I can create a smoothed mask from a volume label?
And then once I create the mask, in order to apply the mask from fsaverage to
each individual subject, would I use mri_vol2vol?
Thanks,
Anais
------------------------------
Message: 7
Date: Wed, 9 Sep 2015 09:29:42 +0200
From: jan.sa...@fnmotol.cz
Subject: [Freesurfer] Automaticky: Jan Sanda is out of the office (a
vr?t? se ne 13.9.2015)
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<of5d8cde08.af77cb0d-onc1257ebb.00292c1d-c1257ebb.00292...@fnmotol.cz>
Content-Type: text/plain; charset=windows-1250
Od st 9.9.2015 do ne 13.9.2015 jsem mimo kancel??.
Pozn?mka: Toto je automatick? odpov?? na va?i zpr?vu "[Freesurfer] Functional
connectivity with volume label" odeslanou dne 9.9.2015 0:42:09.
Toto je jedin? ozn?men?, kter? obdr??te v dob? nep??tomnosti t?to osoby.
------------------------------
Message: 8
Date: Wed, 9 Sep 2015 08:35:32 -0400 (EDT)
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_compute_volume_fractions not filling
some sulci properly
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.lrh.2.20.1509090834380.17...@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-7"
Hi Sebastien
it's pretty hard to tell what's going on from a couple of slices. What was the
command line you used? If you upload the subject I'll take a look (I'll need
the exact command lines you ran as well).
cheers
Bruce
On Tue, 8
Sep 2015, Sebastien Proulx wrote:
My images don?t seem to have come out. Here it is again in attachments
instead of inserts.
?
In csf.png, we see that the calcarine was not completely filled with
CSF by mri_compute_volume_fractions.
?
In gm.png, it is instead filled with gray matter.
?
In ribbon.png, we see that the standard freesurfer pipeline did
correctly assigned to same spot to non-gray matter, suggesting that
the problem comes from mri_compute_volume_fractions, and not from some
failure of the surface reconstruction.
?
Thanks a lot for your much needed help and
Have a very good day!
------------------------------
Message: 9
Date: Wed, 9 Sep 2015 12:42:20 +0000
From: "Amlung, Michael" <amlu...@mcmaster.ca>
Subject: [Freesurfer] Help with recon-all
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<b897b38a9f69b844b9925006fefe67e56cb7b...@fhsdb2d11-1.csu.mcmaster.ca>
Content-Type: text/plain; charset="us-ascii"
Hi all,
I am new to FreeSurfer, so this may be a novice question. We are running
recon-all and the script finished without errors for all of our subjects except
for one. I have opened the recon-all.log file to examine the output, but am not
sure where to locate the error. The last thing printed to the terminal window
was a segmentation fault. Would someone be willing to help me interpret my log
file to find where the error occurred. Thanks for the assistance.
Michael Amlung
********************************************
Michael Amlung, Ph.D.
Assistant Professor
Department of Psychiatry and Behavioural Neurosciences DeGroote School of
Medicine McMaster University
Peter Boris Centre for Addictions Research
100 West 5th Street
Hamilton, Ontario L8N 3K7
Canada
Telephone: (+1) 905-522-1155, ext. 39014
Email: amlu...@mcmaster.ca
Web: http://fhs.mcmaster.ca/psychiatryneuroscience/AmlungMichael.html
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------------------------------
Message: 10
Date: Wed, 9 Sep 2015 08:44:24 -0400 (EDT)
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_compute_volume_fractions not filling
some sulci properly
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.lrh.2.20.1509090843110.17...@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-7"
p.s. you can try increasing the resolution of the intermediate volumes using
the -r switch. The default is 0.5. Try 0.25 (although this will take 8 times
the memory and time I think). Make sure to put the -r 0.25 before before the
mandatory options. If this does make things look significantly better please
let us know
On Tue, 8 Sep 2015, Sebastien
Proulx wrote:
My images don?t seem to have come out. Here it is again in attachments
instead of inserts.
?
In csf.png, we see that the calcarine was not completely filled with
CSF by mri_compute_volume_fractions.
?
In gm.png, it is instead filled with gray matter.
?
In ribbon.png, we see that the standard freesurfer pipeline did
correctly assigned to same spot to non-gray matter, suggesting that
the problem comes from mri_compute_volume_fractions, and not from some
failure of the surface reconstruction.
?
Thanks a lot for your much needed help and
Have a very good day!
------------------------------
Message: 11
Date: Wed, 9 Sep 2015 08:46:56 -0400 (EDT)
From: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Help with recon-all
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.lrh.2.20.1509090845400.17...@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-15"
Hi Michael
sure, send us the recon-all.log. We don't get many segfaults, and usually they
are because you ran out of RAM or disk space. Were you running other things on
the machine at the same time? We will need this info:
https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
cheers
Bruce
On Wed, 9 Sep 2015, Amlung, Michael wrote:
Hi all,
?
I am new to FreeSurfer, so this may be a novice question. We are
running recon-all and the script finished without errors for all of
our subjects except for one. I have opened the recon-all.log file to
examine the output, but am not sure where to locate the error. The
last thing printed to the terminal window was a segmentation fault.
Would someone be willing to help me interpret my log file to find
where the error occurred. Thanks for the assistance.
?
Michael Amlung
?
?
?
********************************************
Michael Amlung, Ph.D.
Assistant Professor
?
Department of Psychiatry and Behavioural Neurosciences
DeGroote School of Medicine
McMaster University
?
Peter Boris Centre for Addictions Research
100 West 5th Street
Hamilton, Ontario L8N 3K7?
Canada
?
Telephone: (+1) 905-522-1155, ext. 39014
Email: amlu...@mcmaster.ca
Web: http://fhs.mcmaster.ca/psychiatryneuroscience/AmlungMichael.html
?
------------------------------
Message: 12
Date: Wed, 9 Sep 2015 15:40:33 +0200
From: "Thomas Potrusil" <am-dam-...@gmx.at>
Subject: [Freesurfer] TrackVis Transforms
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<trinity-0996c35e-3597-4c23-ba98-f2c29136e602-1441806032918@3capp-gmx-bs04>
Content-Type: text/plain; charset="us-ascii"
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------------------------------
Message: 13
Date: Wed, 9 Sep 2015 09:51:34 -0400 (EDT)
From: Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] TrackVis Transforms
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.lrh.2.20.1509090948350.20...@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi Thomas - If you have a .mat transform, try dmri_trk2trk to apply it to a
.trk file. You have to specify reference volumes for the input and output space.
Best,
a.y
On Wed, 9 Sep 2015, Thomas Potrusil wrote:
Dear FreeSurfers !!
I?m trying to bring a trackvis .trk file to freesurfer space but fail
completely...
I tried to execute the code descibed on the following page:
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms
and also read the detailes regarding trk-(header)-data described here:
http://www.trackvis.org/docs/?subsect=fileformat
... but without success !
Can you please provide me an example how to successfully use the following code
on my command line:
trk_verts_crs.xyz = trk_verts.xyz / (trkHeader.voxel_size[0],
trkHeader.voxel_size[1], trkHeader.voxel
_size[2])
trk_verts_tkreg = CRS2XYZtkreg * trk_verts_crs I?m very thankful for
your help, thankx a lot, Thomas
------------------------------
Message: 14
Date: Wed, 9 Sep 2015 13:53:21 +0000
From: "Lim, Lena" <lena....@kcl.ac.uk>
Subject: [Freesurfer] Freesurfer/Qdec brain images
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
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<am2pr03mb0851424cf271de7e41268c33c2...@am2pr03mb0851.eurprd03.prod.outlook.com>
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Dear Experts,
I need some help regarding saving the brain images in Freesurfer/Qdec please:
1) Can I save the brain regions shown in Qdec group analysis as other files and
view them in MRIcroN etc or does it only allow us to save the images as tiff
files (inflated medial, inflated lateral, pial medial, pial lateral). How can I
get more images than these 4?
2) Can I see the other coordinates within the cluster of regions besides the
peak? E.g. The cluster spreads from precuneus to the parietal area so can I get
the coordinates for the parietal region as well besides the peak given in the
table (precuneus)?
3) Where can I get info re the BA nos of the brain regions shown in the Qdec
analysis as well please?
Many thanks,
Lena
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