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Hello FreeSurfer Developers,
I need to compute the distance between the center of the mass in grey matter
images and the cortical boundary. Then, I need this spatial-series to be saved
in a csv. It is also possible to save the cortical boundary serie
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Dear freesurfer developer:
I am writing to ask for the pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z.
Could you kindly provide it?
Many Thanks!
Best,
--
Geng
UESTC school of Life Science
University Of
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Hi Andrew,
I see you specified '-nonempty'. 'wm-hypointensity' is probably excluded
because the voxel count is zero. I'm only looking at this from programmer point
of view. I don't know how wm-hypointensity is assigned in recon-all-clinical.
Best,
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You can try '-empty' to see if it reports differently.
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Huang, Yujing
Sent: Thursday, July 20, 2023 9:38 AM
To: Freesurfer support list
Cc: Gopinath, Karthik ; Iglesias Gonzalez, Juan
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Good afternoon,
I'm trying to broaden my neuroimaging software skills with Freesurfer and was
hoping to do the online tutorial. However it asks me for a password when
downloading the zipped file and said to email to receive the password.
Would it be
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Was that caused by using short? Ie, if you don't use short, is there
still a problem?
On 6/20/2023 10:21 AM, Ruifeng Dong wrote:
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Hi Douglas,
Thanks. Out of curiosity, I kept the short data type in the
mri_conv
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There is nothing that allows it from freeview. The easiest thing to do
is probably to split the annot into labels (mris_label2annot), then load
the label you want with :label=your.label
You can take snapshots automatically with freeview using the -ss o
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recon-all died immediately after trying to create a symlink. Might be
because it is on a VBox. Rob, can you help figure this out?
On 6/21/2023 11:55 AM, Varun Chandran wrote:
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p.s. I am wondering whether this spe
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Do what? If you want to run mri_sclimbic_seg, then just run something like
mri_sclimbic_seg --i input-t1.mgz --o sclimbic.mgz
On 6/21/2023 2:13 PM, Ahsan Ali wrote:
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Dear Greve,
How did you do with this line of
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I think it should work ok. If you want to run it in native space, add
-conform-dc (but this should be done for everyone in your study).
Conforming like this was started in FS 25 years ago and for
reprodicibility purposes, we've kept it there by defau
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You can add -synthstrip in 7.3+ to use synthstrip instead of watershed
On 6/21/2023 5:53 PM, Ruifeng Dong wrote:
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Thank you, Douglas and Malte!
In terms of mask volume, synthstrip and watershed method in FS7.3.2
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The F.mgh is the F ratio and you can use mri_segstats to extract the
means of it.
On 6/23/2023 9:11 AM, Lyna Mariam El Haffaf wrote:
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Dear FreeSurfer team,
We are conducting a study with the ADNI database using
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you can also use the python equivalent so you're not trying to run mex
files
https://secure-web.cisco.com/1g8E_AOm3VXmhvpy6veMl40Kme1LNWWT1lb_WgkRyBt5Etmh-v8ma6TKJSQWDj5TH-KVfoGp0346fsQdTj15hy3nF8ALVxGteNWCIMe8wGmljgqEaDxSxez7d2aqs5WYVsvWzMc3YIBWkKtNAU
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which part do you want to fix? the command not found or the lack of
clusters?
On 6/28/2023 6:25 PM, jordan wagner wrote:
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Hello,
My name is Jordan and I am working on cluster correction between two
groups. I ra
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Can you send the recon-all files from two of your runs that give
different results? BTW, we do these kind of tests weekly and everything
always comes out identical
On 6/28/2023 9:14 PM, 神保岳大 wrote:
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Dear FreeSur
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Have you looked at this page
https://secure-web.cisco.com/1BV2hYoaSBjdqCI3ji_zfSci2RFzSKvskUEpLSzz9KZZmJ3W692xmbGJZYtcILbXwSeNGChMfif4QJenV0WIKvqU9-y6rwrLkf3PY6_kwKAA0UMsTELNqJZjOgJBdeZO_ohao1RiTq7M-MGJ54JDw6BQyJbBIkgZZ28P8CWJqFlnQxggUkQBtLaA1W-aXp2lULZ
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There is not an easy way to do this. You can convert your input to ascii,eg,
mri_convert --ascii+crsf input.mgz output.ascii
Then find the vertex numbers that correspond to your label (visible in
the .label file)
On 7/1/2023 7:06 AM, Akansha Mahesh
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Have you looked at
https://secure-web.cisco.com/1NC9Ltlp5uFU4Bul7SCRlbytQ23JMTs-YMiQzOu_NzomIa6nZaL9N2mnqsU-fD7m65HPlwySDLBF7P8y72mvWmJ2cqFY4Q7A-kc1lN34GNhVG7fhEbEjZ2nYpAGNhmTTP2u0r0ez1W6LHo-mzvMTgdai1mZ1lM0h09SynVVI3ISzORb1Igp1gKBl4FgILzFcDTDs0HWClx0i
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I don't know. I don't think anyone has done a study on it. You'd have to
label the pil de passages in a bunch of subjects and see if the pattern
holds.
On 7/4/2023 7:05 AM, Federica Santacroce wrote:
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Hello Free
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Not sure. My guess is that it is because TicFemale only has 5 subjects
and you are trying to compute 4 parameters from them, leaving only 1
DOF. If you want more help, please send the design matrix (Xg.dat) --
you sent the contrast matrix.
On 7/5/2
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It has stalled on the fixing of topological defects. My guess is that it
trying to fix a large topo defect. It may eventually fix it or it may
time out. If the later, you'll have to fix it yourself by editing the
wm.mgz or filled.mgz. See for example
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Look in ?h. mpm.vpnl.annot
The label is hOCv3
On 7/5/2023 4:22 AM, 周乐晴 wrote:
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Dear Sir,
I can find Visual_v3_d cortex area in FreeSurferColorLUT.txt.
but I was confused that where I can find the result file of
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we do not publicly release this data
On 7/6/2023 12:39 PM, vinuyan sivakolunthu wrote:
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Hello Freesurfers,
I was trying to access the Buckner40 dataset. There is a fswiki page (*MailScanner has detected a possible
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It should not be that pixelated. My guess is that slicer is doing some
kind of smart interpolation to make it look better. One way around it
would be to map your input to the conformed space and run mri_segstats
on that
On 7/6/2023 3:57 PM, Fahad Ha
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Hello Varun,
The Windows file system, i.e., NTFS, does not support soft links. So you
cannot set SUBJECTS_DIR to storage mounted from your Windows machine that has
been formatted by Windows OS, and then run something in the linux VM that is
going t
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First of all, you are not going to get the same answer from these
different programs. For ento, recon-all will zero the thickness in some
areas around ento, and clinical is probably not doing that. Still a
factor of 4 seems pretty large. Maybe Karthik
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On 7/10/2023 10:00 AM, Maria Czarnecka wrote:
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Dear Sisters and Brothers in neuroscience,
I have a problem with conjunction analysis. I do my analysis using:
/mri_concat --i con1/sig.nii.gz --i con2/sig.nii.gz --
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YOu can cite
https://secure-web.cisco.com/1VIvVtvtPygSOcOAqEDVp3ktJYVDLZ2uNCjYhaz-F36ge-CBq7pqvIXuv32zddkOzQdLLzVXYxin8mV7JsE2OIz1hS-4kI6pZ9OizIDuAqOfjm_-NGYVMESz4RhzdSBC8lqRRWQPo0QjEZG7CIJAcklXyt_iwvo0bnzzC5TloHXk_QiOc_3k7id7UQ3W02-MA8Xy_tqVHv-hbO-P-fT
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yes
On 7/14/2023 4:15 PM, Carlos Alcocer wrote:
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Thank you for your response. If I wanted to calculate the surface area
of this cortical ROI, would i pass lh.area.pial into ? Do i still
use --accumulate flag?
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Hi Andrew,
We do not currently support wm-hypointensities with recon-all-clinical runs.
The synthseg based segmentation saved as aseg.mgz will not contain this label
and thus your asset.stats has no information on this.
Karthik
On Jul 20, 2023, at
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Can you load the wmparc along with the surface in freeview? Also send
the recon-all.log file. Is it possible that you ran recon-all several
times on this subject? Eg, the surfaces might not have been good in that
chunk, so you fixed them and reran, bu
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I don't know what you mean. can you elaborate?
On 7/18/2023 11:51 AM, Magang Visa wrote:
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can we use freeview for comparing 2 MRI in a overlaying 3D model in
one windows ?
best regards
_
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I'm not sure what you mean, like some kind of service where you upload
your image and it returns a freesurfer analysis? Not that I know of
On 7/19/2023 1:09 AM, Gonzalo Rojas Costa wrote:
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Hi:
Is there a free
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I'm not sure I understand what you are asking for. Do you want to
compute the distance from a given point in the volume to the closest
point on cortex?
On 7/20/2023 7:09 AM, alexandra.ko...@uksh.de wrote:
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Hello
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Hi, I have a question about the FreeSurfer 7.4.1 release. A couple weeks
ago I added 7.4.1 along with its sha256 checksum to spack (which uses the
centos7 binaries atm) after checking the md5 hash that is provided on the
downloads page. The sha256 was i
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Hello,
We are trying to process a scan with a failed talairach. We have been able to
visualize the misalignment and attempted to use the following command
(tkregister2 --s PI163 –fstal) to manual adjust the talairach.xfm based on the
tutorial
(http
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Hello,
We are trying to process a scan with a failed talairach. We have been able to
visualize the misalignment and attempted to use the following command
(tkregister2 --s PI163 –fstal) to manual adjust the talairach.xfm based on the
tutorial (FsTut
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I think a change was made to the privileges on a single file in the
archive. Gzip subsequently may have changed the modification time in the
updated archive and so the checksums could be different. The checksums
listed on the release page are up t
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The distance between the center of the mass in the GM images and the points in
the outer boundary in the GM images.
Thanks for the quick reply.
Dr. -Ing. Alexandra Korda
Forschung & Lehre
Zentrum für Integrative Psychiatrie ZIP gGmbH
Campus Lübeck
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