Hi Gina
for volumetric structures such as the ventricles it doesn't make sense to
measure thickness. We also don't do it for hippocampus as there is too much
internal structure that we can't model at in vivo resolutions.
The volumes should be in the various stats file in the stats subdir for
Check out the ROI analysis tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials
It's highly recommended that you upgrade to a more recent version of freesurfer
- 5.0 is a decade old.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.
Dear FreeSurfer Developers,
I am trying to measure hippocampal, ventricle and temporal lobe volume &
thickness. Could you let me know the coding?
Freesurfer Version : 5.0, unix
Have a good weekend.
Gina
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During the functional analysis in FS-FAST, are the external regressors
convolved with the hemodynamic response function?
Thanks,
Reza
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Hi Z K,
Thanks. I had thought that the recon-all speed will run much slower on the
external HD but 10 hours seems to be the average recon-all time so I am
pleasantly surprised.
Best Wishes,
Shane
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I wouldn't say that it IS recommended to run recon-all on an external
hard-disk, but in theory this should be fine. There may be a bit of an
I/O bottleneck but I would think with the USB3.0 interface it wouldn't
be too bad.
On 02/17/2017 03:06 PM, Shane Schofield wrote:
> Hello,
>
> I am new t
Hello,
I am new to image analysis and I have a basic question: is it recommended to
run recon-all on external hard-disks (USB3.0) to save space on my laptop? Will
there be any issues with regards to the performance of recon-all? I have just
finished a recon-all on 1 subject and it took me 10 ho
Ah, scale x100 (not -0.1 to 0.5 but -10 to 50). I'm embarrassed I didn't
notice this earlier, All solved and works beautifully, thank you very very
much!
2017-02-17 18:21 GMT+01:00 Douglas N Greve :
> When you click on the different areas, is the value displayed in the
> control window correct?
Hello,
I'd like to suggest an alternative, for anyone interested in going faster than
4 hours. I can't verify compatibility from a technical standpoint, but GNU
Parallel (https://www.gnu.org/software/parallel/) has worked fast and run to
completion reliably when batching multiple recon-all subj
Thank you for this helpful response!
One follow-up question - I realize that images should be processed using the
same version and OS. For my current study, all images but one have been
processed on a previous version of FreeSurfer and it will not be possible for
me to process this one remainin
When you click on the different areas, is the value displayed in the
control window correct?
On 02/17/2017 09:55 AM, Johannes Klene wrote:
> Dear dr. Greve,
> thank you, this looks exactly like what I need. I have created the mgh
> file as suggested in the matlab script, with my stats values
>
In the image comparing the subfield segmentation for versions 5.3 and 6.0 found
at https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields, the
segmentation by version 6.0 does not capture a gray segment that 5.3 includes,
located superior to the other regions. Was it omitted by 6.0 b
Dear FS users
I also work with FS6 and MacOSX 10.7.5 and the left upper panel of Freeview
does not appear at all, ie.e is empty compared with former Freeview versions
(see screenshot).
When I load a volume, it also crashed. Both problem appear also on Mac OSX
10.10.5
Thanks in advance
Regards
Or would it be possible to send us the full crash report?
> On Feb 17, 2017, at 10:17 AM, Z K wrote:
>
> Hi Dan. Is there an error output to the screen or terminal window? We
> will probably need that to help diagnose the issue.
>
>
>
> On 02/17/2017 05:31 AM, Daniel Carey wrote:
>> Dear All
Hello Jared,
Curious... Can you try processing this particular subject with a single
thread and see what happens? If the problem persists let me know and I
will take a look at the subject.
-Zeke
On 02/17/2017 08:28 AM, Jared Saletin wrote:
> Hi Freesurfer gurus:
>
> I recently installed 6.0.0
Hi Dan. Is there an error output to the screen or terminal window? We
will probably need that to help diagnose the issue.
On 02/17/2017 05:31 AM, Daniel Carey wrote:
> Dear All,
>
> I've recently installed FS 6.0 on Mac (OS 10.7.5), and have been unable
> to load volumes in Freeview. When selec
What browser are you using? My first recommendation would be to try
downloading using another browser. If the problem persists than its
probably due to some type of file size limit on the network you are on.
On 02/17/2017 07:25 AM, Jose Enrique Romero Gómez wrote:
>
> Hello,
>
> I'm trying to do
Dear dr. Greve,
thank you, this looks exactly like what I need. I have created the mgh file
as suggested in the matlab script, with my stats values (correlations,
ranging from -0.1 to ~0.5) as 'annotvals'. After updating to FS6.0 i also
managed to get the tksurferfv command to run (tksurferfv fsave
Dear freesurfer-community,
I want to compare cortical thickness in a group of Alzheimers patients's to
healthy controls. Therefore I ran qdec setting the threshold to Min:1.3,
Max:5 (assuming this would give me a significance level of p<=0,05). When I
extract the cortical-thickness-data for the RO
Hi Freesurfer gurus:
I recently installed 6.0.0 on MacOS 10.12 and recon-all is exiting with an
error in mris_smooth. It looks like a library issue.
A prior post had the same issue and indicated uninstalling the whole
distribution and re-installing 6.0.0 fresh (as opposed to installing over 5.
Hello,
I'm trying to download FS6 but always get a timeout error.
This is the link I'm using:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
And this is the error message
*Connection to 132.183.202.158 failed.*
The system r
Dear All,
I've recently installed FS 6.0 on Mac (OS 10.7.5), and have been unable to load
volumes in Freeview. When selecting 'File > Load volume', the dialog box
appears, but when I select any T1.mgz and click Ok, Freeview immediately
crashes.
Has anyone encountered this same issue?
Best wis
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