Hi Xiaoqian,
We don't typically recommend this, but it looks like you will need to edit your
brain.finalsurfs.mgz to account for the wm lesion. I tested this out by filling
in the lesion with 110 and recreating the wm surface -- it seems to work quite
well.
Once that is done, you can run the f
Hi Miguel!
I'll be happy to help with your issue, but I'm having trouble finding your
subject's directory on our server. Could you please try and upload the data via
FTP, again? Also, have you tried either of Bruce's suggestions?
Thanks,
Bram
Bram R. Diamond, BSc
Research Technician II
Laborat
Hi Julia,
I've taken a look at the data you sent us last week and it looks like the issue
is stemming from the topology fixer. If you look through the input scan you've
given us, you can see that the contrast between wm/gm is especially low in
certain regions. This low contrast to noise ratio i
): 617-726-6598
From: Renew Andrade
Sent: Thursday, December 20, 2018 10:12:31 AM
To: Diamond, Bram Ryder
Subject: Re: FreeSurfer: trouble processing subjects
External Email - Use Caution
I don'tknow if I understand right. I don't have a dicom format f
Hi Rosalia,
Within the FTP interface, you need to write "put two_different_problems.txt".
It seems like you only wrote the file name. Also, the example we provide is
"filename.txt", make sure you write your file name - only include ".txt" if
your file has that extension.
Let me know if you h
ine, but the problem starts at mri_convert
function, which surprisingly gives no error. Is it possible for you to look at
the 001.mgz and rawavg.mgz files and see what could be the problem with the
mri_convert function?
Best,
Batuhan
On Sat, Dec 1, 2018 at 12:54 AM Diamond, Bram Ryder
mailto:brd
freesurfer@nmr.mgh.harvard.edu
Cc: batuhan.er...@umram.bilkent.edu.tr; astev...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz
External Email - Use Caution
Done
On Fri, Nov 30, 2018 at 8:46 PM Diamond, Bram Ryder
mailto:brdiam...@mgh.harvard.e
der using PASV.
150 Ok to send data.
226 Transfer complete.
61572 bytes sent in 0.15 secs (402.3777 kB/s)
Best regards,
Batuhan
On Thu, Nov 29, 2018 at 5:36 PM Diamond, Bram Ryder
mailto:brdiam...@mgh.harvard.edu>> wrote:
I can't see any of your data. The problem is likely that you are fee
y subject folder directly via Filezilla or the
terminal.
Best,
Batuhan
On Mon, Nov 26, 2018 at 10:23 PM Diamond, Bram Ryder
mailto:brdiam...@mgh.harvard.edu>> wrote:
Hi Batuhan,
I'm trying to access the files now. What is the name of the files/directory
you uploaded? I'm not
ere is for mghRead().
If you inspect the 001.mgz and rawavg.mgz files, you'll realize that they are
corrupted and probably that's why mghRead fails to read rawavg.mgz.
Can you see the files, did I do the file transmission correctly?
Best,
Batuhan
On Wed, Nov 21, 2018 at 7:32 PM
Hi Batuhan,
Can you please upload the BE2 subject data using our ftp file exchange and let
me know the exact command and terminal output when you ran mri_convert?
Info on our ftp file exchange:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
Thanks,
Bram
Bram R. Diamond, BSc
Resear
e CC_*. Do you think
that can fix the middle line?
Thanks,
Maxime
De : freesurfer-boun...@nmr.mgh.harvard.edu
de la part de Diamond, Bram Ryder
Envoyé : 16 octobre 2018 14:36
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Mi
...@ulaval.ca>> wrote:
External Email - Use Caution
Hi Bram,
No worries.
Here is the link : http://gate.nmr.mgh.harvard.edu/filedrop2/?a=al9nxdabh5h
Thanks,
Maxime
On Oct 16, 2018, at 1:11 PM, Diamond, Bram Ryder
mailto:brdiam...@mgh.harvard.edu>> wrote:
Hi Maxime,
anything specific be
needed. I'll be happy to contribute!
Many thanks,
Maxime
De : freesurfer-boun...@nmr.mgh.harvard.edu
de la part de Diamond, Bram Ryder
Envoyé : 11 octobre 2018 13:18
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Ne
Hi Maxime,
I'll take a look at your data and the issue you're having and get back to you
after the weekend.
Best,
Bram
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Maxime Perron
Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer supp
If I used the -bigventricles flag for all my atrophied and large
> ventricles
> patients and not for my
> healthy patients, wouldn't it introduce a bias when further
> statistically
> comparing groups between
> th
t you ensure your aseg.mgz is accurate.
Additionally, it will be useful to have an accurate aseg.mgz for subcortical
analyses.
I hope that answers your question.
Bram
From: Matthieu Vanhoutte
Sent: Friday, September 14, 2018 4:48:36 PM
To: Diamond, Bram Ryd
this before doing the wm.mgz edits I suggested in my previous email.
Best,
Bram
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Diamond, Bram Ryder
Sent: Friday, September 14, 2018 11:07:42 AM
To: matthieuvanhou...@gmail.com
Cc: freesurfer@nmr.m
Hi Matthieu,
I've taken a look through the files you shared with us and I see the poor
surfaces in the posterior right hemisphere you were referring to in your
message. It looks like your subject has a combination of abnormally large
ventricles and significant wm abnormalities, so I'm surprise
Hi Elena,
I've taken a look through the files you shared with us and can only find the
complete subject directories for sub-90188_run-01_T1w and sub-90310. The
subject directory for sub-01262 (and 209 other subjects) is empty. Could you
please send another link with the subject directory for s
Hi Dr. Kevin Aquino - could you please upload the entire subject directory? At
first glance, it looks like fs is incorrectly including gm in the wm.mgz just
superior to the surface errors you're seeing - the cluster of voxels w/
intensity 250 around the coordinate 87 178 97 in the wm.mgz.
Try e
Hi Jason,
You can use mri_binarize to extract a wm-hypointensities.mgz volume and view
that over the orig.mgz. The following will make a binary volume called
wm-hypointensities.mgz from all voxels in the aseg.mgz with an intensity of 77
- all voxels labeled wm-hypointensities:
mri_binarize
Hi Shadia,
How did you make the externally-derived ribbons? Can you please send us your
recon-all.log and your subject directory so we can take a look?
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
Thanks,
Bram
From: freesurfer-boun...@nmr.mgh.h
false,
despite control points?
I have uploaded the respective files.
Best,
Martin
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Diamond, Bram
Ryder
Gesendet: Mittwoch, 13. Dezember 2017 23:23
An: Freesurfer support list
Betreff:
Hi Martin,
We've taken a look at the scans you uploaded, and unfortunately it won't be
possible to run the standard recon-all on your subject. Recon-all is not
designed to work on scans with such large lesions. If you are interested,
there may be a way to generate a reasonable model of the r
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