External Email - Use Caution
I Think I have a permission. I ran chmod -R u+rwX to make sure, but the error
was the same. Can you confirm from below please?
\mudathirbakhit$ ls -l $FREESURFER_HOME/
total 568
drwxr-xr-x 39 mudathirbakhit admin 1248 Mar 18 20:24 6.0.0
External Email - Use Caution
Douglas,
Thanks again. Is this value in the brainstem.dat file accurate or is it subject
to the same limitation in that the value will depend on the field of view of
volume acquisition?
In other words, is it valid to add this number to the brain to
External Email - Use Caution
The patch (see text below) only directed me to replace a file in the
freesurfer/gcc/lib directory, which I did. Do I also need to replace the
make_average_subject and mri_aparc2aseg files in my freesurfer bin?
*To patch the existing 6.0.0 release you
External Email - Use Caution
Hello Hannah,
While the freesurfer group does not control the port(s) numbers exposed on the
public facing web servers that host the freesurfer web pages, I’ve been told by
IT that you should not need to access the ftp port and you should only need
Hi Noam
You can always use the -rl switch in mri_convert (rl == "reslice
like"). So for example
mri_convert -rl rawavg.mgz orig.mgz orig_back_to_raw.mgz
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Peled, Noam
Sent: Tuesday, April 6, 2021 2:52 PM
To:
Hello,
I was running recon-all on a raw T1 image with the following properties:
dimensions: 126 x 144 x 88
voxel sizes: 1.78, 1.78, 1.78
Orientation: PSL
Besides the raw T1, I have other nii files with the same dimensions and
orientation that I want to visualize on top of the
External Email - Use Caution
Postdoctoral Fellow position available at Albert Einstein College of Medicine
in NYC
The departments of Neuroscience (Dr. Elyse Sussman) and Radiology (Dr. Mark
Wagshul) at the Albert Einstein College of Medicine in New York City are
seeking a
Hi Ornaith
The mapping uses the vertex index. That is, the vertex index is stored in the
flatmap, so you should always be able to recover it, then look up the location
of that vertex on any other surface (of the same hemisphere/subject)
Cheers
Bruce
From:
External Email - Use Caution
Hello FreeSurfer developers,
Thanks a lot for your help. I have initialised the pialxyz the way you
suggested and made the flatmap in MatLab using the read_patch function
(screenshots attached). I still don't understand how to convert between
the
Thanks for the details. We’ll look into it a bit and get back to you.
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Cook, Philip
Date: Monday, April 5, 2021 at 11:42 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] "ERROR: crypt() returned null with 4-line file"
Hi Katja,
Okay good to know. I will follow up off-list.
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Zoner, Katja
Date: Tuesday, March 30, 2021 at 1:24 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] [External] Re: "ERROR: crypt() returned null with
External Email - Use Caution
Thank you Douglas, I tried quickly via correcting my gtmseg.ctab output
with standardized for gtmseg only for tissue types, it runs without error,
I will create a new look up table and try further.
Thanks again,
Kind regards.
On Tue, Apr 6, 2021 at
External Email - Use Caution
We are wanting to connect to the site in the need of support from the
freesurfer website (i.e. the manual pages) while behind our closed system.
On Tue, Apr 6, 2021 at 9:29 AM Douglas N. Greve
wrote:
> why do you need to connect to the web site?
External Email - Use Caution
Dear Douglas
Thank you very much for your suggestions.
Regards
Ramesh
On Tue, 6 Apr, 2021, 7:03 PM Douglas N. Greve,
wrote:
> Twice the same image at 1x1x1, then use mri_robust_template to register
> and average them together
>
> On 4/6/2021 8:10
It is expecting a voxel shift map, which won't work with topup. One
thing you can do is to do the preprocessing (motion correction, slice
timing correction, topup) outside of fsfast, save the output as
something like f.mypreproc.nii.gz, then specify -funcstem f.mypreproc
when running
External Email - Use Caution
Hi Doug,
Did you have a chance to look at this subject ?
Thanks a lot,
Julie
-- Forwarded message -
From: Julie Ottoy
Date: Thu, 18 Mar 2021 at 13:08
Subject: Re: [Freesurfer] Failed tissue type check {Disarmed}
To: Freesurfer
gtmseg will not give an error, but the color table that gtmseg outputs
will not be right and needs to be fixed.
On 4/6/2021 9:41 AM, Bahar Hazal Yalçınkaya wrote:
External Email - Use Caution
Thanks for response, color table and annotations are there
"--ctx-annot
Anything with 0 thickness is assumed to not be a valid cortical vertex.
As such, we don't smooth it so that it does not corrupt other vertices
that are valid. When you stack the images together and use this masked
smoothing, any invalid vertex will become 0 for all subjects and will be
ignored
External Email - Use Caution
Hello,
We are looking at the vertex-wise thickness measures for participants within
the fsaverage space. There are a number of indices within the cortex that have
thickness values of 0 in the thickness.fsaverage.mgh surface files. In
FreeSurfer
Twice the same image at 1x1x1, then use mri_robust_template to register
and average them together
On 4/6/2021 8:10 AM, Ramesh Babu wrote:
External Email - Use Caution
Dear Eugenio and Philipp,
Thank you very much for your suggestions. Could you please give more
input on "acquire
Do you have write permissions to
/Applications/freesurfer/subjects
Of not on a mac
On 4/6/2021 6:39 AM, バキット・ムダシル wrote:
> External Email - Use Caution
>
> Hi,
> I am trying to make an average subject but when the process reaches
> mris_average_surface it fails as seen below.
> My
why do you need to connect to the web site? that is not needed to run FS
On 4/5/2021 3:20 PM, Swearingen, Hannah wrote:
External Email - Use Caution
Hi,
I am setting up an Access Control List for an isolated VLAN in which
my center's neuroimaging computing workstations will be
It is normal that those give different results. I would expect them to
be extremely close to each other, so small that the difference does not
matter. But if you had to take one, I'd take the output of
mris_anatomical_stats
On 4/5/2021 11:47 AM, Alberto Del Cerro Leon wrote:
You will need to create a new color table. This is not hard, but not
easy either. First, there should be a color table already there. I'm not
sure what that will be like; it might have your segments in it, it might
not. It might be easier to run gtmseg with the standard options and look
at the
Hello,
Please remove me from the free surfer forum mailing list.
Thank you,
Katherine
Katherine Coleman, MS
Research Assistant II
Mood Trajectories and Outcomes Laboratory
Department of Psychiatry
[cid:image001.jpg@01D6CE33.2A446E30]
___
Freesurfer
Can you send /tmp/banu.tmp.decompressed.dcm.1TXZUy.dcmdjpeg.out ?
If that is not there any more, run it again and send the newly created file
On 4/4/2021 3:57 PM, Banu Femir wrote:
External Email - Use Caution
Dear Freesurfer Developers,
I'm trying to analyze a set of MRI data that I
So the problem is that there are spaces in the path? That will probably
cause a lot of FS to fail
On 4/2/2021 11:30 PM, zalewk wrote:
External Email - Use Caution
Hi freesurfer team,
I've tried running recon-all as mentioned before with the -xf flag
under different conditions.
As
The "-make" functionality does not work in V7. We should have disabled
that flag
On 4/2/2021 3:41 AM, Marion DURTESTE wrote:
External Email - Use Caution
Dear FreeSurfer developers,
When running*recon-all -make all *after correcting a few errors from
the recon-all output, it exits
Run it with -debug as the first option, capture the output, and send it
to us.
On 4/1/2021 8:29 PM, zalewk wrote:
External Email - Use Caution
Hi Freesurfer team,
My lab recently switched over from FS6 to FS7 and I think I've
encountered a bug with recon-all.
I'm running subjects
I don't understand, please elaborate
On 4/1/2021 2:00 PM, miracle ozzoude wrote:
External Email - Use Caution
Hello Experts,
I did like to extract wm whilst retaining the label ids. I tried
mri_extract_labels but it didn't work.
Any help would be appreciated.
Many thanks,
Paul
Include the flag -cw256 with recon-all!
On 4/1/2021 1:52 AM, Amar Shukla wrote:
External Email - Use Caution
Dear Team,
Actually I am trying to test my own data in recon all , but i have
taken only one subject for recon. It shows me this error.
ERROR! FOV=408.000 > 256
Include the
The format is not correct. It should be
Input SubjectID Class
You have SubjectID in there twice
On 4/1/2021 1:15 AM, Ishi Tandon AIB, Jaipur wrote:
External Email - Use Caution
Hello FS experts,
I attempted to execute mri_glmfit on my structural data through the
following command -
Did you check that the bold is really in register with the anat? You can
do this with
tkregisterfv --mov bold_preproc.nii.gz --s sub-01--reg deleteme.lta --surfs
On 3/31/2021 10:49 AM, Karan Desai wrote:
External Email - Use Caution
Hi FS Forum,
I am following up on this post
External Email - Use Caution
Dear Eugenio and Philipp,
Thank you very much for your suggestions. Could you please give more input
on "acquire the T1WI double and average it after coregistration, this
increases the SNR".
Should aquire twise the same sequence with 1x1x2 voxel
External Email - Use Caution
Hi,
I am trying to make an average subject but when the process reaches
mris_average_surface it fails as seen below.
My command was as follow:
make_average_subject --out avgsubject --subjects spl_01 spl_02 spl_03 spl_04
spl_05 spl_06 spl_07 spl_08
35 matches
Mail list logo
