Thanks for your reply Yaniv! That is how I initially tried loading the
NIFTI volumes (via the GUI, File|Load), but in the meantime I discovered
what the problem was: there were spaces in the name of the folder
containing the image, and apparently non-Windows OSs such as Xubuntu don't
deal well
Thanks Doug,
now it works!!
for mac use
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.mac
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.linux32
doug
On 12/05/2012 05:11 AM, Jos? ?ngel Pineda wrote:
Hi again,
Sure I did
Dear FS team,
After I ran the recon-all to get the total cortical thickness, the volume of
the left hypocampus ( = the number of voxels) equals to 2166 which I
thought should be the total hippocampal volume. But if we add all the
voxel numbers from the hippocampal subfield I will get a much
Hi,
Is it possible to run recon-all on a series of scans?
I have multiple scans that I want to process longitudinally. The .nii files
have all been converted to .mgz files and labelled sequentially (i.e., 001.mgz,
002.mgz, etc.) in /Applications/freesurfer/subjects/subjid/mri. I've tried
Yes,
in 5.2 there should be the two new options --qdec and --qdec-long
to allow passing qdec tables both in the regular cross sectional and in
the longitudinal format in addition to the existing other ways of
passing subjects lists (--s or --fsgd or --f ).
Now care needs to be taken in the
Hi again,
like I said in my previous emails, the measurements from the subfield
tools are based on .5x.5x.5 voxels, so you have to divide them by 8 to
convert them to cubic milliliters. Then, if you add up the volumes from
the subfields (without including the hippocampal fissure), you should get
Hi Doug,
I did surface-based inter-hemispheric comparison.
I used an arbitrary surface data (.mgz) resampled from a volume data (.nii),
otherwise I follow the instruction.
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
I got a good result
Julia, what version of FS are you using? It looks like pre-5.0. Can you
upgrade to 5.1? There were a lot of changes in going from 4 to 5, and it
is becoming increasingly hard to support version 4.
doug
On 12/06/2012 02:45 AM, Julia Foecker wrote:
thanks.
attached the info file.
When I
Shige, it is looking for tables of cluster p-values (the csd files).
When you followed the wiki instructions, did you tell it to use
fsaverage_sym as the target subject? You must have used a subject called
average.
doug
On 12/06/2012 11:53 AM, Shigetoshi Takaya wrote:
Hi Doug,
I did
Hi Natasha, yes, you have to run recon-all separately for each scan.
doug
On 12/06/2012 11:14 AM, Natasha Jawa wrote:
Hi,
Is it possible to run recon-all on a series of scans?
I have multiple scans that I want to process longitudinally. The .nii
files have all been converted to .mgz files
Hi Hubert,
The physical side of the image in fslview is not indicative of the
actual side. You have to look at the little letters on the side to see
what side it is actually on. When you do this, do you see an R or an L?
BTW, you might want to use mris_volsmooth which was written to do this
freesurfers,
i've been using my own scripts to compute tSNR for data i was running
through FSL, but i'm now running the data through freesurfer and i wanted
to better understand what the fsnr volumes spit out by selxavg3-sess are.
i poked around the wiki and mailing archives and couldn't find
Hi Alex,
On 12/06/2012 12:21 PM, Alex Kell wrote:
freesurfers,
i've been using my own scripts to compute tSNR for data i was running
through FSL, but i'm now running the data through freesurfer and i
wanted to better understand what the fsnr volumes spit out by
selxavg3-sess are. i
Thanks for your reply, Doug
After inter-hemispheric registration onto fsaverage_sym using surfreg, I did
not use mris_preproc in my analysis because of the following two reasons:
(i) I thought I can't use --meas because the input is an arbitrary surface
data.
(ii) I don't want to use
The problem is that you have a version 4 analysis that you are trying to
view with version 5 tools. To use version 5 visualization, you'll need
to remake the analysis in version 5 and then reanalyze. Otherwise,
you'll have to use the version 4 stream (instructions attached). It is
somewhat
Hi
I saw an updated version of mri_glmfit in
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/.
Should I update this file in my freesurfer installation.
What do this fix? Is is not in the release notes?
Knut J
___
How can I get 300 dpi resolution or about when saving tiff files in
tksurfer?
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only
Hi Knut
the tiffs written by tksurfer are 600x600 regardless of what DPI you set.
You can change the dpi with convert (or photoshop), but it won't change the
# of pixels.
cheers
Bruce
On Thu, 6 Dec 2012, Knut J Bjuland wrote:
How can I get 300 dpi resolution or about when saving tiff
Perhaps you can maximize the tksurfer window on a large monitor, take a
whole screen screenshot, and then in a photo editing program: decrease the
physical size of the image (in mm or inches) while not decreasing the
matrix size. You can do this in photoshop in Image Image Size And
then change
Hello Martin,
Thanks for your confirmation. I downloaded the last version of
FreeSurfer: the dev5-20120624, from the ..fswiki/LMEModels page, but
there is the old mris_preproc, so I will use the fsgd file.
Thanks for pointing out about the long.base - files!! That was a mistake
of mine. And
If you want to get a figure with arbitrarily high resolution regardless
of the screen size, have a look at PySurfer*. It's not an official part
of freesurfer but can display many of the freesurfer files. It can
produce high resolution figures by moving the camera, taking screenshots
and then
Hi ,
I have winkler variety surface area data that is already smoothed and
converted to vertex wise data on my average subject. Each subject has
a file rh.ico7.fwhm10.mgh, lh... and Doug gave me a way with mri_concat
to assemble the data into a single file so i can run command line mri_glmfit
Hi Alex
Sorry, my bad. You are right. To grab the subjects'ID the correct code is:
sID = Qdec(2:end,1);
I'm going to fix that in the wiki. The new error is due to the numeric value on
the left hand side of
[M,Y,144] = sortData(M,1,Y,sID);
You cannot assign any value to 144. Just change
I'm working with raw timeseries waveform data from a resting state
dataset. There's one run per participant, so no between-run
normalization is required. With Doug's help, I have mastered extracting
the timeseries information from individual ROIs in surface space. The
timeseries data is the
Hi Bruce,
Do you upsample the tiffs from tksurfer when making image for
publications? Or do you use another program in FreeSurfer suite?
Knut J
On 12/06/2012 10:22 PM, Bruce Fischl wrote:
Hi Knut
the tiffs written by tksurfer are 600x600 regardless of what DPI you
set. You can change the
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