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Original message
From: "Greve, Douglas N.,Ph.D."
Date: 10/10/19 5:56 PM (GMT-06:00)
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] brain mask without CSF ...
You will have to do it manually. You can create a binary
You will have to do it manually. You can create a binary CSF mask from the
aseg.mgz using mri_binarize. Don't use 702 and 703 -- those refer to "FSL-FAST"
not "FS-FAST". Try using the --vcsf flag to mri_binarize (ventricular csf).
Then use mri_label2vol to map it into the functional space. Once
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To confirm, your label is starting on the fsaverage surface. You can open
tksurfer fsaverage ?h pial and open the label and it shows up?
From my experience using fcseed-sess & fcseed-config using FS v6.0.0 what
you want to do is move the label from
I think that the wm edits should have worked. Can you load the rh.orig.nofix
and rh.orig to see if they encompass your edits? If not, then maybe your did
not re-run it properly.
On 10/8/2019 12:22 PM, Xiaoqian Yan wrote:
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Dear Freesurfer experts,
I am
This appears to be a bug in mri_label2vol when you specify a surface.
Instead, you can create a volume in the conformed space, and then use
mri_label2vol with that volume as the --seg input. BTW, you should use
mri_label2label to map from fsaverage into the individual subject space,
then do
The easiest thing is probably to set the output value when running mri_binarize
with the --binval option. Eg, left amygdala would be --binval 18
On 10/10/2019 6:09 PM, Gwang-Won Kim wrote:
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Hi there,
I made the 3 ROIs (Thalamus, amygdala, putamen) using
External Email - Use CautionHi there, I made the 3 ROIs (Thalamus, amygdala, putamen) using "mri_binarize".Then, I opened "FreeView" to show the 3 ROIs (3 volumes). I want to show 3 ROIs as different colors in FreeView.I tried to apply to FreeSurferColorLUT in FreeView but 3
Use the patch
On 10/10/2019 11:07 AM, Daniel Westfall wrote:
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Hi Everyone,
I just wanted to double check the current state of processing T3 submillimeter
data with Freesurfer 6. We have two studies: one with 0.9 mm isotropic and the
other with 0.8 mm
Unfortunately, I have no idea. It might be worth contacting matlab support over
this. It seems like others (non-freesurfer) have had this issue, but there
isn't much out there on how to resolve it.
Andrew
From: Iglesias Gonzalez, Juan E.
Sent: Thursday,
Hi David,
nobody can really tell you what will happen if you use the software outside its
tested use cases. 5mm thick slices, with tumor resection is not what it has
been designed to work with. And as I said, gad enhanced also not. It might give
you meaningful results or not. The only way to
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You are really the boss Dr. Iglesias!!
Happy to know Ola is in expert hands :)
Rosalia
El jue., 10 oct. 2019 15:35, Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> escribió:
> Bummer!
>
> Andrew, any ideas on this?
>
> Cheers,
>
>
Bummer!
Andrew, any ideas on this?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: on behalf of Olamide Abiose
Reply-To: Freesurfer support list
Date: Thursday, 10 October 2019 at 15:14
To: Freesurfer support list
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Thank you so much for your quick response. I saw this link and mentioned this
to my server administrator, but he seemed to disagree that that was the source
of the issue. There were definitely permissions issues when he first downloaded
Matlab
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Martin, thank you for these comments. These are extremely valuable!
Although my patients had tumors, these are cured (this is why I have so few of
them…) and have no residual mass effect/deformity beyond biopsy tracks / small
resection cavities.
Dear Ola,
This looks like a very ugly error but someone experienced something similar in
the past and it turned out to be a permissions problem.
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I see, in that case, you should ask directly to Dr Eugenio Iglesias as he
is the one who created this script.
His last known email is: e.igles...@ucl.ac.uk
I am sure he will answer you as soon as possible, but if you see that there
is no answer. Then
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Okay, here it is. I just want to stress that it's not my script, but the
amygdala subfield module released by Freesurfer
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).
I don't have permission to directly edit
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Hi,
Yes, otherwise there is no way to debug the lines in your script.
Best,
Rosalia
El jue., 10 oct. 2019 14:41, Olamide Abiose escribió:
> External Email - Use Caution
>
> Hi Rosalia,
>
> I'm running this as a command line argument,
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Hi Rosalia,
I'm running this as a command line argument, because I'm only testing one
subject. Are you asking for the segmentHA_T1.sh script?
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Rosalia Dacosta
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Hi Olamide,
How to check your line errors without the bash script you are using?
Could you at least send the .sh script?
Best regards,
Rosalia
On Thu, Oct 10, 2019 at 8:29 PM Olamide Abiose wrote:
> External Email - Use Caution
>
> Hello,
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Hello,
I'm having great difficulty running the segmentHA_T1.sh command. I'm using the
latest development version of Freesurfer and have downloaded Matlab R2014b. I
get the following message when I try to run the command. Any advice/suggestions
you
It appears to be a bbregister error:
bbregister --s APOE.269 --init-fsl --dti --mov
/Volumes/DANIEL/dti_pin/trac/APOE.269/dmri/dwi.nii.gz --reg
/Volumes/DANIEL/dti_pin/trac/APOE.269/dmri/xfms/anatorig2diff.bbr.dat --fslmat
/Volumes/DANIEL/dti_pin/trac/APOE.269/dmri/xfms/diff2anatorig.bbr.mat
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Dear FreeSurfers!
I would like to confirm something before I proceed with my analyses. I think I
am just confused again.
I am doing resting state analysis using fsfast. I am trying to use a label
defined in the fsaverage space as a seed using the
Hi,
according to this page:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview ,
there is a separate protocol to correct cerebellar errors with rois such as the
lingual gyrus, fusiform and etc specially the creation of the
brain.finalsurfs.manedit file. I have a few
Hi all,
Our primary archive for all posts to the mailing list can be found at:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu
And we've now disabled the public 'pipermail' archives, which include anything
under:
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer
If you come
Hi Maxine,
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ contains
executables and a README file that details how you can patch your freesurfer
install to fix this issue.
best
Andrew
From: on behalf of Maxime Perron
Reply-To: FS Help
Date: Friday, September 6, 2019
Hi Himanshu,
Our pub disk went down a while ago and we lost the 6.0 patch files, but I've
just updated that link with the necessary executables and README file.
Following the readme instructions should fix your issue.
best
Andrew
From: on behalf of Himanshu Aggarwal
Reply-To: FS Help
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Dear colleagues,
*apologise for cross posting*
Brainhack Global 2019 is collecting registrations for hosting sites! The
event will be run globally, on November 13-17, to share ideas and
experiences with colleagues across diverse disciplines and
External Email - Use Caution
Hi Everyone,
I just wanted to double check the current state of processing T3
submillimeter data with Freesurfer 6. We have two studies: one with 0.9 mm
isotropic and the other with 0.8 mm isotropic. After doing some
investigating, I found that there
External Email - Use Caution
Hello,
It isn't an error with recon-all, at least I don't think it is. Recon-all
ran without error and the file that Tracula is trying to access seems to be
where it is supposed to be. It seems like Tracula is having an issue
opening the lh.white
Hi Daniel - is this an error in recon-all? Then I wouldn't put "tracula error"
in the subject line if you want the developers of the structural stream to look
into it.
a.y
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Daniel Callow
Sent:
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Hello,
I am running tracula on some of my DTI data and have had no issues for most
of my subjects. However, for one of them I get the following error after
mri_segreg
MRISread(/Volumes/DANIEL/freesurfer_pin/APOE.269/surf/lh.white): could not
open
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Hello Jonathan,
It could help to add -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON to the cmake
command line to see what the compiler is doing when you run make and see the
first instance of those errors, but
clearly something is not right with the linker
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