HI,
Im using freesurfer newly, i have a folder of a subject's MRI's named
139942
I tried to run recon-all of a File named I000 The point is to get
Superior temporal gyrus thickness.
but it show an error and stop working. i looked up archive of FAQ's but i
didnt anything usefull.
There i
Hi Doug and co.,
To follow up about this: I may have resolved the issue. For posterity, label
names of the mris_convert --parcstats should be created without the
"ctx-?h” prefix:
My parcstats file previously read...
ctx-lh-bankssts 0.905
ctx-lh-caudalanteriorcingulate 0.838
ctx-lh-caudalmiddl
you can use the command:
set_current_threshold_from_percentile(min, mid,max)
which will compute the thresholds based on the histogram of values
On Tue, 3 Mar 2015, Douglas N Greve wrote:
>
> I'm not sure what you mean. optimal in what sense?
> doug
>
> On 03/03/2015 03:21 PM, Hirsch, Gabriella
Am 03.03.2015 um 14:42 schrieb Douglas N Greve :
>
> Some of this Martin will have to comment on, but my comments below
>
> On 03/03/2015 12:35 PM, Janosch Linkersdörfer wrote:
>> Hey Doug,
>>
>> thanks again! That means, I would do something like:
>>
>> 1.) construct longitudinal qdec table
It looks like you made your txt file under windows which creates an
obscure situation where there are carriage returns instead of line feeds
and that causes the error. If you run 'more my_parcstats.txt' you see a
bunch of ^M strings. So, you'll need to recreate it under a linux system.
doug
O
I'm not sure what you mean. optimal in what sense?
doug
On 03/03/2015 03:21 PM, Hirsch, Gabriella wrote:
> Hi Fs experts,
>
> I had a quick question about settings thresholds of surface overlays
> in Tksurfer. I am currently generating images of the thickness, volume
> and surface area of indiv
You can use something like
rawfunc2surf-sess -i fstcmc -hemi lh -fwhm 5 -o
fstcmc.sm05.fsaverage.lh.nii.gz
Then in mkanalysis-sess, use -funcstem fstcmc.sm05.fsaverage.lh (and do
not include preprocessing options)
doug
On 03/03/2015 02:12 PM, Jan Willem Koten wrote:
>
> Dear Surfer experts,
Some of this Martin will have to comment on, but my comments below
On 03/03/2015 12:35 PM, Janosch Linkersdörfer wrote:
> Hey Doug,
>
> thanks again! That means, I would do something like:
>
> 1.) construct longitudinal qdec table
> - only use fsid, fsid-base, and years/age columns
> - substract
Hello Freesurfers,
I recently updated my Freesurfer version and now I am getting an error in
tracula.
awk: cmd. line:1: fatal: cannot open file `1000' for reading (No such file
or directory)
Any help would be appreciated.
trac-all.error
Description: Binary data
Mon Mar 2 18:24:56 CST 2015
/ho
Hi Giedre,
Small intersections like that are fine and won't affect the lGI computation, so
you are good with that. Values around 20 are however more preoccupying! Can you
send me a screenshot of the lGI overlaid on the surface for this subject using
tksurfer or freeview?
Best,
Marie
NB: if
Dear Surfer experts,
(Most likely Dough)
It is common practice to perform the slice time correction first and than the motion correction. However free surfer seems to work in the opposite way.
I have tried to write a mini matlab freesurfer script for the common way.
system(['stc-ses
Hey Doug,
thanks again! That means, I would do something like:
1.) construct longitudinal qdec table
- only use fsid, fsid-base, and years/age columns
- substract the average age of the one-time point subjects from years/age value
for every subject at every time point
2.) run long_mris_slopes
-
Hi Doug,
Thanks! the combination of sampling incorrectly and confusion of spaces was the
root of the problem.
Everything is now looking as it should.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Do
That is the right way (or one of them). Did you look at the result in
tksurfer?
On 03/03/2015 11:34 AM, Jin, Tony wrote:
> Hi all,
>
> I’d like to map my own stats (one value per Desikan-Killiany region)
> onto a subject's surface file, to create a figure similar to the
> following:
> http://o
Hi all,
I’d like to map my own stats (one value per Desikan-Killiany region) onto a
subject's surface file, to create a figure similar to the following:
http://openi.nlm.nih.gov/detailedresult.php?img=3280212_pone.0031913.g001&req=4
To do this, I tried to create a "scalar overlay file" using mri
I don't know, esp since it is an approximation to begin with. An
alternative is to take the offsets from your multi-time-point subjects
and the single maps from your subjects with one time point and run that
through the one-sample-group-mean (--osgm in mri_glmfit). If you go this
route, then y
I think just using DOSS instead of DODS will do it (--fsgd your.fsgd doss)
On 03/03/2015 12:42 AM, Anders Hougaard wrote:
> Thanks Doug.
> Any suggestions for a more appropriate design?
> I guess this is a common situation where two or more parameters only
> apply to one group (in this case pati
On 03/03/2015 10:43 AM, Sarah Finnegan wrote:
> The command I used to visualise the label converted to volume form (using
> mri_label2vol) in tkmedit was
>
> tkmedit V2_subject5_1 orig.mgz -overlay V2_lh.mgz -overlay-reg
> register.dat -fthresh .5 -fmid 1
>
> my tksurfer command was
> tksurfe
Hi Antonin, please remember to send responses to the list. Thanks! I've
put a new version of cluster-sess in that same location. Let me know if
that works.
for the mri_mcsim command, make sure to pass it a fwhm that is an
integer. Also, I would probably just run it with --fwhm-max so that it
d
The command I used to visualise the label converted to volume form (using
mri_label2vol) in tkmedit was
tkmedit V2_subject5_1 orig.mgz -overlay V2_lh.mgz -overlay-reg register.dat
-fthresh .5 -fmid 1
my tksurfer command was
tksurfer V2_subject5_1 lh inflated
where I then attempted to ove
Hi Carolina,
the command long_qdec_table reduces your longitudinal table (the one with the
second column 'fsid-base') into cross sectional format with one line per
subject. That's all it does. In order to create the within-subject rate and
percent change maps, you need to run long_mris_slopes f
On 3/3/15 9:41 AM, Sarah Finnegan wrote:
> Hi Doug,
>
> Thanks I had hoped to use mri_mask but was foiled in my attempt to convert
> the .label files to .mgz using mri_label2bvol. I assumed I must be on the
> wrong track.
>
> my command was
>
> mri_label2vol --label V2_lh.label --temp f.nii.g
Hi Doug,
Thanks I had hoped to use mri_mask but was foiled in my attempt to convert the
.label files to .mgz using mri_label2bvol. I assumed I must be on the wrong
track.
my command was
mri_label2vol --label V2_lh.label --temp f.nii.gz --reg register.dat
--fillthresh .3 --proj frac 0 1 .1
Thanks Martin. It works now.
On Mon, Mar 2, 2015 at 10:51 PM, Martin Reuter
wrote:
> Hi Bishesh,
>
> it is a know bug. in your recon-all find this block (should be in line
> 6148)
>
> if ( ! $found_tpNid ) then
> echo "ERROR: $tpNid is not in
> ${longbasedir}/${BaseSubjsListFn
Hi Martin,
Thanks for your instructions. In my analysis when we look at Two Stage
Model results within our control group , we see increase in thickness
(thickening) more than decrease (thinning), where we expect to see the
thinning effect. Is there any explanation for this? I have 19 controls with
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