The actual time between tp1 & tp2 varies for subjects, *but* every subject
received the same "dose" of treatment between timepoints. To ask if the
treatment changed a subject's cortical thickness, I'm not using the actual
time difference, I'm using a constant 1 for the time difference. (i.e. in
lon
Hello freesurfer gurus,
We acquire 2 BRAVO T1s on a GE 3T during the same scan session on most of our
study participants, but because of various issues, occasionally only get 1
T1/participant. I've been processing the data combining both T1s when we have 2
and using just 1 T1 when that was all
Is the time between tp1 and tp2 the same for all subjects? If not, are
you using that information?
On 03/21/2014 04:15 PM, Peggy Skelly wrote:
> The overall question is: did the cortical thickness of healthy
> hemispheres (of stroke subjects) change from tp1 to tp2, and does it
> correlate wit
The overall question is: did the cortical thickness of healthy hemispheres
(of stroke subjects) change from tp1 to tp2, and does it correlate with the
change in their functional measure? So I was using the long.thickness-rate
measure and qdec.
Peggy
On Fri, Mar 21, 2014 at 1:38 PM, Douglas N Gre
Hi Elizabeth,
The measure called "CorticalWhiteMatterVol" *is* the total cerebral white
matter.
See this page:
http://freesurfer.net/fswiki/MorphometryStats
The values for the "{lh,rh}CorticalWhiteMatterVol"measures in aseg.stats
used to be the same as that returned by the 'mris_wm_volume' functi
You could also do it the following way: (you need to download dcmtk)
Assuming you have a bunch of files called MR.*
for dicom in MR.*
do
dcmodify -m "(0010,0010)=PatientsName" ${dicom}
dcmodify -m "(0010,0030)=MMDD" ${dicom}
done
This backs up all the dicoms (they become "MR.*.bak"),
Thank you for your response. But just to clarify a bit further, in the
asegstats2table there are values given for TotalGrayVol. I am assuming this
includes both subcortical and cortical measures for GM along with cerebellar
values, etc. Likewise, I am looking for TotalWhiteVol or a way of calcul
Thank you Doug. I was using the same label file for all subjects before. I
will create the labels for each individual and run the
mris_anatomical_stats ( I tested it on one subject that didnt run before,
and it did not give any errors this time)
Thanks again!
Rupa
It looks like this label w
mri_label2label needs to be called with --surfreg fsaverage_sym.sphere.reg
Martin, can you modify long_mris_slopes to add this?
But another question is exactly what you want to do in the end. What
function of the slopes and hemisphere are you trying to compute?
doug
On 03/21/2014 01:20 PM, P
I tried your suggestion (using subjTP/xhemi in place of subjTP) in the qdec
table. I doesn't work because long_mris_slopes uses subjTP and subjBase to
create "subjTP.long.subjBase", the directory of the actual data. Extra
slashes "/" in the name create an incorrect name (i.e.
subjTP/xhemi.long.subj
Ok sorry, new to this mailing lark, will post to mailing list :-)
Thanks
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: 21 March 2014 15:56
To: Cha
Is it just when you use the MIP or whenever you view it? Are the values
between 0 and 255?
doug
On 03/20/2014 01:28 PM, Borzello, Mia wrote:
> picking the electrode points for an intracranial patient. I can usually do it
> pretty easily in tkmedit, but I'm just getting an odd contrast with this
yup, that's it
thanks Caspar
Bruce
On Fri, 21 Mar 2014, Caspar M. Schwiedrzik wrote:
Thanks to all that have replied so far!
Bruce, are you referring to this: http://freesurfer.net/fswiki/BIRND-UP ?
Thanks, Caspar
2014-03-20 17:40 GMT-04:00 Harms, Michael :
Hi Caspar,
I can't address your qu
When you say the MNI305 space, do you mean the 2mm space that is the
output of FSFAST? If so, then first run reg-mni305.2mm to create the
appropriate registration file. Then use this registration file when
running mri_vol2vol
doug
On 03/20/2014 02:39 PM, Omar Singleton wrote:
> Hello Freesurf
Hi Charnjit, that script is Maria's code I think (which is why it is a
good idea to post to the list and not to us personally :-)
doug
On 03/21/2014 07:28 AM, Charnjit Sidhu wrote:
> Hi Doug,
>
> I think the problem is similar to the following post on the mailing lists:
>
> https://www.mail-arch
yes, try that and see if it resolves the problem
On Fri, 21 Mar 2014, Anita
van Loenhoud wrote:
> Hi Bruce,
> The wm.mgz was created a while ago with an older version, by another
> student.
>
> At the moment I use v5.3.0. Should I recreate wm.mgz with this more recent
> version, or is there anot
you can get it from this page. You don't need the other files unless you are
doing the interhemispheric analysis
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 03/21/2014 04:41 AM, N. Medic wrote:
> Dear Doug,
>
>
> I would need the mris_preproc patch, however the link provided
> (ftp://surfer
Thanks to all that have replied so far!
Bruce, are you referring to this: http://freesurfer.net/fswiki/BIRND-UP ?
Thanks, Caspar
2014-03-20 17:40 GMT-04:00 Harms, Michael :
>
> Hi Caspar,
> I can't address your question regarding a specific tool, but wanted to
> mention a note of caution.
> Yo
Hi Bruce,
The wm.mgz was created a while ago with an older version, by another
student.
At the moment I use v5.3.0. Should I recreate wm.mgz with this more recent
version, or is there another option?
Thank you,
Anita
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On Thu, Mar 20, 2014 at 5:58 PM, Chris Watson
wrote:
> FYI, you can also get the first file like this:
>
> first_file=$(tar ztf ${in_file} | head -1)
Not to beat this to death, but sometimes this returns a directory name
instead of a file name. So `find -type f` is safer, unless there's
some way
Hi Francesco,
Given that the recon pipeline is built on an adult atlas it is not
expected to work for such young subjects. In the past, with high quality
images, we managed to get reasonable recons for ages down to 4 (or
sometimes 3). For the younger population though it will not work. We are
Hi Anita
mris_anatomical_stats isn't a flag to recon-all. It is it's own binary
that you should call directly from the command line.
For the znzTAGskip error, this was a bug we briefly had but hasn't been
around in a long time. Can you try downloading a new version? What version
did you use t
Hi Bruce,
See below. Thank you!
Anita
First I tried:
*aloenhoud@somerenserver:/data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050$
*mris_anatomical_stats -mgz -f stats/lh.aparc.stats -b -a
label/lh.aparc.annot -c label/aparc.annot.ctab 0050 lh pial
INFO: assuming MGZ format for volumes.
co
Huh, will you look at that:
$ time find s04_epi -type f |sed 1q
s04_epi/s04_epi.0001
real 0m0.096s
user 0m0.002s
sys 0m0.014s
$ time tar tf s04_epi.tar.gz |sed 1q
s04_epi/s04_epi.0001
real 0m0.016s
user 0m0.001s
sys 0m0.008s
Thanks! (Also, modern 'tar' seems to figure out compression on its
ow
Dear Doug,
I'm very thankful for your helpful comments! I will check the feat2surf script
and apply it to map FSL-data in individual and common space (preconditions:
existing FEATdir with non-smoothed EPI's and applied reg-feat2anat). I will
make use of the -projfrac 0.5 to sample in the middle
Hi Anita
you need to include the full command line and screen output for us to
help you.
cheers
Bruce
On Fri, 21 Mar 2014, Anita van Loenhoud wrote:
Hi mailinglist,
I want to obtain aparc.stats for pial instead of white matter surface area.
I read that I therefore should adjust mris_anatomic
Hi mailinglist,
I want to obtain aparc.stats for pial instead of white matter surface area.
I read that I therefore should adjust mris_anatomical_stats. However, when
I run this command separately, the following error occurs:
cannot allocate memory
Then I tried to put autorecon3 -parcstats in fr
Dear Doug,
I would need the mris_preproc patch, however the link provided
(ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc) is
not working. Is there another way of getting the patch (rather than downloading
the new version of FreeSurfer)?
Best wishes,
Nenad
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