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Thanks for your reply Eugenio. I renamed a few files in the /mri folder:
aseg.mgz → aseg.1mm.mgz
aseg.hires.mgz → aseg.mgz
brain.mgz → brain.1mm.mgz
brain.hires.mgz → brain.mgz
filled.mgz → filled.1mm.mgz
filled.hires.mgz → filled.mgz
norm.mgz →
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Hello Praveen,
The first line of dcmunpack script should indicate it calls the tcsh
interpreter. However, neither csh or tcsh interpreters are installed by
default on Ubuntu. The "which" command will probably report it is not
found on your system t
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Hi experts,
While running recon-all on subjects with 3T T1 scans, I ran into an error
with one subject during skullstripping stage. Recon-all was running with 3T
flag.
The error message is the following:
register_mri: find_optimal_transform
find_opti
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Hi Freesurfer developers,
Sorry if I'm making a simple mistake that I've overlooked. I am currently
trying to do the freesurfer tutorials available at
http://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials and am having problems
with the dcmunpack command
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Dear FreeSurfer Developers:
I compared the thickness, area, volume in the mild traumatic brain injury
patients with health control by FreeSurFer, and found a statistic difference
region in the cortex area, I defined the statistic difference regio
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Hello, After i asked a question, why can't I receive a reply from others
in my mailbox?___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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hello,
Previously, rh.white and rh.aparc.2009s.annot were used to generate vertex_id
and vertex_label,
'
from freesurfer_surface import Surface
from freesurfer_surface import Label
from freesurfer_surface import Annotation
surface = Surface.read_tri
Make sure to use "subjlist", not "sublist". If that is not the issue, then
please attach your log file and configuration file - it's hard to guess the
issue without more information.
Best,
Anastasia.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Sha
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I am getting this error near the tail of the 7.1.0 recon-all.log file just
before exit:
ERROR: find_corresponding_center_FSformat did not complete successfully!
At this link from May 13:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.
Hi Julia,
This is a small bug that's been fixed in the 7.1.1 patch release. I would
recommend updating freesurfer versions (there will be no differences in
recon-all results).
Best,
Andrew
On 10/13/20, 8:44 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Julia Lam" wrote:
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Hello,
I have been trying to run trac-all on a DWI of a participant, but I keep
getting the error "run list is longer than subject list"
I have created a configuration file setting sublist and runlist to just one
subject so I am not sure what the err
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Hi Doug
I'm analyzing the gyrification values between schizophrenia and healthy
volunteers. While performing group analysis in QDEC, I encountered an error
when setting the smoothing (fwhm) parameter to 25.
Here is the error message from the terminal o
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Thank you very much, I will try surface analysis with command in 7.1.1 version
-原始邮件-
发件人:"Wang, Ruopeng"
发送时间:2020-10-20 00:39:56 (星期二)
收件人: "李梦君"
抄送: "Freesurfer support list"
主题: Re: [Freesurfer] Problem of the Mapping Label to the Subje
Sorry I was commenting on the screenshots in your previous email. I thought
they were from freeview. We do not support Qdec anymore in 7.x versions.
Ruopeng
On Oct 19, 2020, at 11:09 AM, 李梦君
mailto:meng...@csu.edu.cn>> wrote:
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Thanks for your help, I have
Try using the correction for multiple comparisons (mri_glmfit-sim). Set
the CWP threshold to 1.0 to get all the clusters. It will create a table
with GI values for each cluster. Run mri_glmfit-sim with --help and/or
look on line to get more info
On 10/14/2020 3:55 PM, Basavaraju, Rakshathi wr
There is no QDEC in 7.X, we have abandoned it.
On 10/19/2020 11:09 AM, 李梦君 wrote:
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Thanks for your help, I have tried FS 7.1.1, while there is no Qdec
command when I tried FS 7.1.1 in the terminal window. How should I
start the Qdec in the 7.1.1 version.
We are no longer support tksurfer. You can try using freeview. If you
run tksurferfv, it will run freeview with most of the tksurfer command
line options
On 10/14/2020 11:42 PM, Kothapalli, Satya wrote:
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Hi Expert,
I am trying to render the surface maps u
With 6 classes and 3 variables, you will have 24 regression coefficients
and so 24 items in your contrast matrix (so good, so far). The order will be
1. MaleMaxT-Offset
2. MaleKahn-Offset
3.
4.
5.
6.
7. MaleMaxT-AgeSlope
8
9
10
11
12
13 MaleMaxT-HRSD_Reduction-Slope
14 MaleKahn-HRSD_Reduction-Slo
I don't know. Each command will have an fs_time output which will have a
measure of the peak memory used, though it is not super accurate.
Alternatively, I could add something to mri_fuse_segmentations to
periodically print out the peak memory usage
On 10/13/2020 3:01 PM, Paul Wighton wrote:
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Thanks for your help, I have tried FS 7.1.1, while there is no Qdec command
when I tried FS 7.1.1 in the terminal window. How should I start the Qdec in
the 7.1.1 version.
Best wishes
Mengjun Li
-原始邮件-
发件人:"Wang, Ruopeng"
发送时间:2020-10-19
You have to run recon-all on your T1-weighted image (see the tutorials
on the wiki), then run the hippo/amyg segmentation as found here
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
On 10/13/2020 12:32 PM, Elena Aggius-Vella wrote:
External Email -
We don't use qdec anymore, so I can't remember what the interface is
like. You can transfer your coordinates to fsaverage space, see
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
and then go to that point in freeview
On 10/13/2020 9:45 AM, Paul Dhami wrote:
External Ema
I don't understand what you are saying. Can you elaborate?
On 10/13/2020 8:31 AM, 1248742467 wrote:
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hello, FreeSurfer
I have loaded rh.pial and rh.aparc.2009s.annot, why my version does
not have the label view option that can see the annotation? Is it a
Use mris_label2annot
Run with --help to get examples
On 10/13/2020 8:22 AM, 1248742467 wrote:
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hello, After I updated the vertex_label of rh.aparc.a2009s.annot with
an algorithm, now I want to replace the vertex_label in the .annot
with the updated vertex_
What happens if you don't include --segno ?
On 10/13/2020 8:11 AM, Rovai Antonin wrote:
> External Email - Use Caution
>
> Hello,
>
> when using asegstats2table with the two flags --etiv and --no-vol-
> extras, I get the following error:
>
> ERROR: --etiv, cannot find EstimatedTotalIntraC
On 10/13/2020 5:42 AM, Maron M. wrote:
> External Email - Use Caution
>
> Dear Freesurfer Team,
>
> I need to move an atlas file, Shen268 in 2mm
> (https://www.nitrc.org/frs/download.php/7977/shen_2mm_268_parcellation.nii.gz)
> from volumetric into surface space in order to do some anal
Not sure, we don't use tksurfer that much anymore. Have you tried
freeview? You can run freeview with tksurferfv and the same tksurfer
arguments (makes it easier)
On 10/13/2020 5:03 AM, Marina Fernández wrote:
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Dear Freesurfer experts,
I would like to mod
No sure what you are trying to do. Each vertex on the surface has
several coordinates associated with it. Eg, a given vertex on the white
surface will have a coordinate in the volume space (see
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems); that same
vertex in the ?h.sphere.reg
Load it as a volume using freeview
On 10/11/2020 4:42 PM, Valentina Mancini wrote:
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Thank you for this answer.
How should I load aparc a2009+aseg.mgz for visualization and load a
color map with p-values?
If I load the fsaverage with the command "tksurf
That is fine. The surface has to cross the ventricle at some point
On 10/9/2020 2:09 PM, Julie Ottoy wrote:
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Dear Freesurfer team,
I have a question regarding the freesurfer delineation of the subject
in attachment. Here the pial delineation crosses the ve
Can you send the recon-all.log file?
On 10/9/2020 12:47 PM, Kathy L. Pearson wrote:
> External Email - Use Caution
>
> No, it does not exist, and my question is why not in 7.1.0 when it is created
> with the same two commands in 5.3.0?
>
> Thanks,
>
> Kathy
>
>
>> Douglas N. Greve Fri, 0
Those control points are still in gray matter.
Please remember to post to the list, thanks
On 10/9/2020 11:18 AM, Kazuki Sakakura wrote:
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Thank you for continuously helping me.
With your comment, I performed to put some control points in WM
(attached image
On 10/8/2020 8:31 PM, Gwang-Won Kim wrote:
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Hi there,
I obtained a seed region (left superior frontal)from anatomical
data to process resting state fMRI data as follows: fcseed-sess -o
lh.SFC.dat -segid 1028 -s session -fsd rest.
I wonder if what the see
I think this is a bug in freeview from FS 6.0.0 that has been fixed in 7.x.
Would it be possible for you to try FS 7.1.1? A quick workaround you may try
first is to change the offset for the inflated surface to 0 0 0 in freeview
6.0.0.
Best,
Ruopeng
On Oct 19, 2020, at 2:38 AM, 李梦君
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