for left and right:
1. 2 and 42
2. 3 and 42
3. 10 and 49
4. 77/78/79
5. 11 and 50
6. 12 and 51
7. 13 and 52
8. We don't have a single one for all of cingulate and it depends on which
parcellation you use. You should take the uniton of e.g. 1002 and such
(assuming you are using the aparc and not
FYI, these numbers come from $FREESURFER_HOME/FreeSurferColorLUT.txt
On 1/7/15 9:19 AM, Bruce Fischl wrote:
for left and right:
1. 2 and 42
2. 3 and 42
3. 10 and 49
4. 77/78/79
5. 11 and 50
6. 12 and 51
7. 13 and 52
8. We don't have a single one for all of cingulate and it depends on
which parc
Hi Amanda
it depends what you are doing. They will certainly distort thickness
estimates in those regions. It is really, really hard to get rid of dura
unless you acquire data for that purpose. If you have a highres FLAIR or T2
or a multi-echo mprage we have tools for automatically avoiding it
Make sure that you are looking at the surfaces though. It looks like the
image you attached was the aseg.mgz, and you should not be using the
"cortex" as defined in the aseg.mgz because that is based on the
volume-stream segmentation. Either overlay the surfaces, or take a look
at the aparc+aseg
You can get that program from here
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/5.3.0-patch/lion/3dvolreg.afni
copy it into $FREESURFER_HOME/bin
doug
On 01/07/2015 05:14 AM, std...@virgilio.it wrote:
> Hi list,
>
> I'm running FS-FAST.
>
> After this command
>
> preproc-sess -sf sess
Mmm, there may be something wrong. Can you send the log file
scripts/trac-all.log?
On Wed, 7 Jan 2015, Giovanni de Marco wrote:
Hi Anastasia,
trac-all -prep is running for 8 hours (all the night) and it doesn't stop.
Please, see the attached file.
How long does trac-all take ?
Should I che
Hello Bruce,
Thanks for the suggestion! I've never used control points to bring intensities
down, but I suppose they do normalize the selected voxels to an intensity value
of 110.
There are also a few voxels of what to my eyes appear to be tentorium that are
labeled as white matter. Can you th
Hi Anastasia,
Thanks for your response. I have sent over a zip file via the filedrop portal,
it seemed to fail each time I tried to send it to
freesurfer@nmr.mgh.harvard.edu so I've sent it over to your email address -
hopefully you have received this.
I've had a look at the segmentations and
Hi Michael and Bruce,
Thanks for your help. This does look a lot better when I look at the
aparc+aseg.mgz.
Thanks,
Amanda
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Harms, Michael
Sent: 07 January 2015 15:43
To: Freesurfer support lis
Hi Amanda - See attached screenshot of your data, there is a gross
misregistration (~45 degree angle rotation) between the diffusion and
anatomical. You can check if this is the case for the rest of your bad
cases by superimposing the FA map (dmri/dtifit_FA.nii.gz) and anatomical
segmentation
Hello,
I sent in a message yesterday but to no avail. I thought I would add a little
more info about the error message I'm receiving. I am trying to view surfaces
in 3D using Freeview on my own subject data via this script from the Freesurfer
website (replacing the subject name);
freeview -f
Can you try just loading one surface? Such as:
freeview -f /media/seagate_external/subject/surf/lh.inflated
Does it load? What if:
mris_info /media/seagate_external/subject/surf/lh.inflated
or even just:
ls -l /media/seagate_external/subject/surf/lh.inflated
Does it show any error?
On 01/07
Hi,
We would like to know if there a method available to segment a freesurfer
surface into a given number of parcels such that each parcel has the same size
(i.e. the same number of vertices).
Many thanks for your help!
Best wishes,
Charmaine
---
tentorium is tough depending on the details of the scan
good luck
Bruce
On Wed, 7 Jan 2015,
Douglas Merkitch wrote:
Hello Bruce,
Thanks for the suggestion! I've never used control points to bring
intensities down, but I suppose they do normalize the selected voxels to an
intensity value of 11
p.s. although labeling tentorium as wm shouldn't matter as long as there
is no connection to the body of the cerebral wm
On Wed, 7 Jan 2015, Douglas
Merkitch wrote:
Hello Bruce,
Thanks for the suggestion! I've never used control points to bring
intensities down, but I suppose they do normalize
Hello freesurfer community!
I am interested in using the warpfield produced in freesurfer talairach.m3z
to warp coordinates from fsaverage space to subject space(mainly for
subcortical so no sphere involved).
For that I was wondering how to read the warpfield or how to convert it to
mgz nifti or s
Please be advised,
This message contained one or more of the following prohibited file types:
(.zip,.bat,.exe,.pif,.scr). The file(s) have been automatically removed from
the message, in order to protect the privacy of our patients and employees, and
to protect the integrity of our systems and
Please be advised,This message contained one or more of the following prohibited file types: (.zip,.bat,.exe,.pif,.scr). The file(s) have been automatically removed from the message, in order to protect the privacy of our patients and employees, and to protect the integrity of our systems and data
Please be advised,
This message contained one or more of the following prohibited file types:
(.zip,.bat,.exe,.pif,.scr). The file(s) have been automatically removed from
the message, in order to protect the privacy of our patients and employees, and
to protect the integrity of our systems and
What does the gradient table look like? Based on these errors, it may not
like that there is no 0 before the decimal point:
printf: -.89: expected numeric value
printf: -.004202: expected numeric value
printf: -.001857: expected numeric value
On Wed, 7 Jan 2015, Giovanni de Marco wrote:
This is not a plain text file. What format is it in?
On Wed, 7 Jan 2015, Giovanni de Marco wrote:
it looks like thats in attached file
2015-01-07 21:55 GMT+01:00 Anastasia Yendiki :
What does the gradient table look like? Based on these errors, it may not
like
that there is no 0
Format txt
2015-01-07 22:08 GMT+01:00 Anastasia Yendiki :
>
> This is not a plain text file. What format is it in?
>
>
> On Wed, 7 Jan 2015, Giovanni de Marco wrote:
>
> it looks like thats in attached file
>>
>> 2015-01-07 21:55 GMT+01:00 Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>:
>>
with trac-all I used these two files in attached file.
2015-01-07 22:15 GMT+01:00 Giovanni de Marco :
> Format txt
>
> 2015-01-07 22:08 GMT+01:00 Anastasia Yendiki >:
>
>>
>> This is not a plain text file. What format is it in?
>>
>>
>> On Wed, 7 Jan 2015, Giovanni de Marco wrote:
>>
>> it look
I can see what the name of the file is, but try running "more" on it or
opening it with a text editor.
On Wed, 7 Jan 2015, Giovanni de Marco wrote:
Format txt
2015-01-07 22:08 GMT+01:00 Anastasia Yendiki :
This is not a plain text file. What format is it in?
On Wed, 7 Jan 2015
Actually I use this gradient file (diffusion60directions.txt) below with
Trackvis and everything is fine.
0 0 0
-0.164494 0.018226 0.98621
-0.190456 0.462978 -0.865666
-0.730086 0.629388 0.266169
-0.613388 -0.746602 0.257566
0.306915 0.919394 -0.246004
0.317328 -0.847873 0.424753
0.965395 0.127917
Can I use this txt file for trac-all ?
2015-01-07 22:27 GMT+01:00 Giovanni de Marco :
> Actually I use this gradient file (diffusion60directions.txt) below with
> Trackvis and everything is fine.
>
> 0 0 0
> -0.164494 0.018226 0.98621
> -0.190456 0.462978 -0.865666
> -0.730086 0.629388 0.266169
>
Thank you very much.
I have placed file 3dvolreg.afni in Applications/freesurfer/bin/ but the error
persist.
Stefano
Messaggio originale
Da: std...@virgilio.it
Data: 7-gen-2015 11.14
A:
Ogg: [Freesurfer] Error first step FS-FAST
Hi list,
I'm running FS-FAST.
After this command
Great, then copy these values into a new plain text file (not rich text
format), run it through tracula, and let us know what you get.
To give you any idea of what I see when I run more on the
diffusion60directions.txt that you attached:
% more diffusion60directions.txt
"diffusion60directio
Please,
Could you tell me if this file is better ? I used textwrangler on Imac
2015-01-07 22:36 GMT+01:00 Anastasia Yendiki :
>
> Great, then copy these values into a new plain text file (not rich text
> format), run it through tracula, and let us know what you get.
>
> To give you any idea of wh
This is a plain text file, yes.
On Wed, 7 Jan 2015, Giovanni de Marco wrote:
Please,
Could you tell me if this file is better ? I used textwrangler on Imac
2015-01-07 22:36 GMT+01:00 Anastasia Yendiki :
Great, then copy these values into a new plain text file (not rich text
format),
did you rehash?
On 01/07/2015 04:35 PM, std...@virgilio.it wrote:
>
> Thank you very much.
>
> I have placed file 3dvolreg.afni in Applications/freesurfer/bin/ but
> the error persist.
>
> Stefano
>
>
>
> Messaggio originale
> Da: std...@virgilio.it
> Data: 7-gen-2015 11.14
> A:
> Ogg: [F
And is it executable?
On 01/07/2015 04:35 PM, std...@virgilio.it wrote:
>
> Thank you very much.
>
> I have placed file 3dvolreg.afni in Applications/freesurfer/bin/ but
> the error persist.
>
> Stefano
>
>
>
> Messaggio originale
> Da: std...@virgilio.it
> Data: 7-gen-2015 11.14
> A:
> O
Thanks Anastasia.
I try to rerun trac-all tomorrow. I let you know.
Giovanni
2015-01-07 22:50 GMT+01:00 Anastasia Yendiki :
>
> This is a plain text file, yes.
>
> On Wed, 7 Jan 2015, Giovanni de Marco wrote:
>
> Please,
>> Could you tell me if this file is better ? I used textwrangler on Imac
>
How can I check whether it is executable?
Thanks,
Setafno
Messaggio originale
Da: gr...@nmr.mgh.harvard.edu
Data: 7-gen-2015 22.51
A:
Ogg: Re: [Freesurfer] R: Error first step FS-FAST
And is it executable?
On 01/07/2015 04:35 PM, std...@virgilio.it wrote:
>
> Thank you very much.
>
>
ls -l and see if the 'x' bit is set. For example:
ls -l mris_register mris_register.c
-rwxrwxr-x 1 fischl fsdev 21563282 Jan 6 17:02 mris_register
-rw-rwxrw- 1 fischl fsdev37035 Jan 6 17:02 mris_register.c
mris_register.c is not and mris_register is executable
cheers
Bruce
On Wed, 7
Ja
-rwxr-xr-x 1 root wheel 60776 Jan 29 2013 #trac-all#
-rw-r--r--@ 1 Stefano staff 3985520 Jan 7 21:21 3dvolreg.afni
ls -l mris_register mris_register.cls: mris_register.c: No such file or
directory
-rwxr-xr-x 1 root wheel 7351544 May 14 2013 mris_register
Thanks,
Stefano
Dear FS experts,I got into a trouble when used the command of mri_vol2surf.I
planned to project a volume file (left hemisphere) onto the surface (lh) of the
same subject. While i got nothing (value=0 for nearly all the vertexes except
for a few valued vertexes on the medial surface). However, i
Hi list,
I'm running FS-FAST.
After this command
preproc-sess -sf sessid -surface fsaverage lhrh -mni305 -fwhm 5 -per-run -fsd
rest
I obtain this error:
register-sess completed
Sess01 MC -
mc-sess -fstem f -fmcstem fmcpr -s Sess01 -d
/Applications/freesurfer/subjects/
Dear Freesurfer Gurus —
I’m using mri_extract_label to extract segmentation masks, but a little baffled
as to which label numbers to use for each brain part.
The masks I need are:
1. Global white matter
2. Cortical Gray matter
3. Thalamus
4. WM-Hypointensity
5. Caudate nucleus
6. Putamen
7. Pal
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