Thanks Doug,
I already downloaded the new script for mri_label2vol, but it seems it is
just compiled for linux, as I cannot execute it in my Mac. If it is so,
could you please upload another compiled for mac, or source.
Thanks
Jose
> For the missing insula problem, try using a newer version of
I have noticed that when I reconstruct the brains (with edits) three files
appear; fsaverage, lh/EC_average and rh.EC_average...I only recently
noticed these and have before then been under the impression that all the
useful data for analysis is in each individual's subject folder. Therefore
I have
Hi all. I have a question regarding the use of freesurfer + fs-fast
preprocessing to apply the Lausanne 2008 parcellation scheme to some
structural data, and then extract from those ~1000 ROIs the average time
series from a 4D resting state functional run.
I'm posting what I have carried out s
Dear FS team,
I would like to know which subfield ( left_presubiculum, left_CA1,
left_CA2-3, left_fimbria, left_subiculum, left_CA4-DG,
left_hippocampal_fissure) contribute to the head, body and tail of left
hippocampus.
It also seems that the first column of nonPartialVolumeStat
Doug,
I am also curious about this mri_label2vol upgrade. Will this work on the
Windows virtual machine version of FreeSurfer? I downloaded and placed it in
the FREESURFER/bin directory, but when trying to run it I receive an error that
states: Exec format error. Binary file not executable. Tha
Hi Chris, you're almost there. There are a few mods I'd make to your stream:
1. You can run preproc-sess -s subXX -fsd rest -surface self lhrh -fwhm 0
(without the -mni305 since you are working in the subject's anatomy)
2. mri_segstats \
--annot subXX lh myaparcPXX \
--i $FUNCTIONALS_DIR/subX
Hi Cathy
they are used during the recon to map labels from average spaces into
your individual subject (e.g. entorhinal cortex).
cheers
Bruce
On Tue, 4 Dec 2012,
Catherine Bois wrote:
> I have noticed that when I reconstruct the brains (with edits) three files
> appear; fsaverage, lh/EC_aver
Jose, try this one
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.mac
doug
On 12/04/2012 09:06 AM, José Ángel Pineda wrote:
> Thanks Doug,
>
> I already downloaded the new script for mri_label2vol, but it seems it
> is just compiled for linux, as I cannot execute it i
Hi Jose, did you set the permissions to be executable?
chmod a+x mri_label2vol
doug
On 12/04/2012 11:34 AM, Sarosh, Cyrus wrote:
>
> Doug,
>
> I am also curious about this mri_label2vol upgrade. Will this work on
> the Windows virtual machine version of FreeSurfer? I downloaded and
> placed it
Hi Julia, I meant tksurfer-sess (not surf-sess)
doug
On 12/04/2012 05:39 AM, Julia Foecker wrote:
> Hi Doug,
> thanks for your reply.
>
> I got the following messages when running the
>
>
> surf-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE
> -retinotopy polar
>
> and there
Hi Freesurfer experts,
This week a read the article of Bernal-Rusiel et al. titled "Statistical
analysis of longitudinal neuroimage data with Linear Mixed Effects models". In
this article you described the submission of single time-point scans to the
longitudinal pipeline of Freesurfer. I'm ver
Doug,
I am unsure if Jose did this in his attempts to get it to work, but I ran this
command after downloading and receiving this error initially and even after
running this command I still receive the same error in the Windows virtual
machine version of FreeSurfer. Any other ideas?
Thanks,
C
Dear Doug,
I would like to the same thing that Kelsi (as I read the post) asked about:
For patients with a lesion in one hemisphere, I want to compare the
hemispheres with lesions to the contralateral hemispheres without lesions.
I think that your answer below is a recipe for comparing right and
Hi Henk-Jan,
to avoid bias between subjects with single time points and others, we
run them through the same steps. This way it is possible to include them
into the statistical analysis. (For this an artificial base is created
with the head in an upright and straight position).
This feature will
Hi Negar,
from your log file:
build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.1.0
Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009
i686 GNU/Linux
So it looks like you are running the 32bit free surfer version which will be
limited to >= 4GB addressable memo
Hi Antonella,
The volume given by the hippocampal subfield tool is in .5x.5x.5 voxels.
Therefore, to convert to cubic millimeters, you need to divide by 8.
Regarding the sufield <-> A/P question, the only correpondance is
"Left-Hippocampus" <-> left tail and "Right-Hippocampus"<->right tail
Cheers
Hi Anders,
Run mris_preproc twice :
# For the left-lesioned subjects
mris_preproc --target fsaverage_sym --hemi lh
--xhemi --paired-diff \
--srcsurfreg fsaverage_sym.sphere.reg \
--meas thickness \
--out LeftLesionSubjects.lh.lh-rh.thickness.sm00.mgh \
--s Lsubj1 --s Lsubj2 ...
#
Hi Sebastian,
Thank you for your reply. The virtual machine that I'm using was built by a
friend who also uses FreeSurfer and I copied it entirely onto my computer
(a huge folder, 263GB). Freesufer works just fine for him. So whatever
version of Freesurfer he's using, it's working for him and I'm
Hi Negar,
On Dec 4, 2012, at 12:19 , Negar Memarian wrote:
> Hi Sebastian,
>
> Thank you for your reply. The virtual machine that I'm using was built by a
> friend who also uses FreeSurfer and I copied it entirely onto my computer (a
> huge folder, 263GB). Freesufer works just fine for him.
Hi Kristina
your arrows are pointing at the hippocampus which is not neocortical and
not intended to be modeled by the surfaces
cheers
Bruce
On Tue, 4 Dec 2012, Kristina
Nalbandian wrote:
Hello,
I am having some problems editing the volume created after the -recon-all
-all function in
Hi all,
I am looking for an accurate method of calculating whole brain volume (WBV)
from a spreadsheet of FS MRI data. I had previously been using the following
method:
1. Sum the following: CSF, lateral ventricles, 3,4,5 ventricles, and the
choroid plexus
2. In a second column, sum the follow
Hi Kristina,
More info here:
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Thesurfacesnearthemedialwall.2Chippocampus.2Candamygdalaaren.27taccuratelyfollowingthestructuresthere.HowcanIfixthis.3F
-Louis
On Tue, 4 Dec 2012, Bruce Fischl wrote:
Hi Kristina
your arrows are poin
Negar,
This appears to be a strange problem. From the recon-all.log file, the
important error is this one:
GCAread(/usr/local/freesurfer/average/RB_all_2008-03-26.gca): couldn't
expand gcs to 1114693712
which means it failed to alloc the 1.2GB needed to load the atlas. but
given that earlier i
Negar,
Another option is to try another vm. While we have our own vm
w/freesurfer Ubuntu instance, people have had success with installing
the FSL VM, which is built with Centos, and then within that download
and install the 64b freesurfer instance. Although the background images
in your attache
Try this one
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.linux32
On 12/04/2012 12:13 PM, Sarosh, Cyrus wrote:
> Doug,
>
> I am unsure if Jose did this in his attempts to get it to work, but I ran
> this command after downloading and receiving this error initially a
Hi Doug,
Thanks for your helpful answer (below) with respect to the use of mri_segstats
on functional activation in subject-specific ROIS.
I have a follow-up question, however, regarding the initial creation of the
ROIs. I am basing my ROIs on the Desikan-Killiany atlas, either using existing
Yes, method #1 will work better.
doug
On 12/04/2012 06:22 PM, Susan Alice McLaughlin wrote:
> Hi Doug,
>
> Thanks for your helpful answer (below) with respect to the use of
> mri_segstats on functional activation in subject-specific ROIS.
>
> I have a follow-up question, however, regarding the i
Dear Freesurfer Experts,
We are analysing longitudinal data - the difference between 2 groups (P
and M) [19 and 17 subjects] with 2 time points for each group (A, B).
We are using the example of "Repeated Measures Anova"
(http://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova)
For our
Hi, did anyone have a chance to see my last e mail? See below, cheers!
Hugh
On 16 November 2012 10:48, Hugh Pemberton wrote:
> Hi,
>
> I have just received this error after a recon-all subjid- ___ all :
>
> ERROR: _FindFacePath: could not find path!
> /home/hughp/freesurfer/subjects/B__
Hi Hugh
this is fixed in 5.2. If you need a fix right away Nick or Zeke can get you
an updated mris_topo_fixer binary
cheers
Bruce
On Wed, 5 Dec 2012, Hugh Pemberton wrote:
Hi, did anyone have a chance to see my last e mail? See below, cheers!Hugh
On 16 November 2012 10:48, Hugh Pemberto
Hi Nick,
On Dec 4, 2012, at 14:41 , Nick Schmansky wrote:
> Negar,
>
> This appears to be a strange problem. From the recon-all.log file, the
> important error is this one:
>
> GCAread(/usr/local/freesurfer/average/RB_all_2008-03-26.gca): couldn't
> expand gcs to 1114693712
>
> which means i
that'd great, cheers!
Hugh
On 5 December 2012 10:29, Bruce Fischl wrote:
> Hi Hugh
>
> this is fixed in 5.2. If you need a fix right away Nick or Zeke can get
> you an updated mris_topo_fixer binary
>
> cheers
> Bruce
>
>
> On Wed, 5 Dec 2012, Hugh Pemberton wrote:
>
> Hi, did anyone have a ch
Hi Alex,
I am not familiar with the way Doug describes the repeated measure anova
on the wiki. Of course in a longitudinal setting repeated measures are
correlated and I am not sure if this is considered in that model there.
Since you have only 2 time points, why not simply compare the difference
Hello Martin,
thanks for the quick reply !
as I understood, from the "LongitudinalTutorial", after long_mris_slopes
the results can be seen for each subject, and in order to see the group
results, all subjects should be analysed in the Qdec, and there I could
see the results for each group, bu
Hi Negar
why don't you upload your dataset (the whole subject directory) and we'll
see if there is anything strange about it. Have you ever completed a
recon successfully? Have you tried running it on Bert's excellent brain?
Bruce
On
Tue, 4 Dec 2012, Negar Memarian wrote:
Hi Nick, Sebasti
Hi Alex,
as far as I know qdec can do what you want (compare e.g. the atrophy
rate across the two groups).
However, you don't need to use qdec for the second stage, you can run
mri_glmfit directly on the differences (or slopes). Basically you get a
thickness_yearly_change (or pct change) in each
Hi Negar,
I guess this is where I have to leave the issue to Nick and Bruce as I am way
out of my league here :). It would have been nice if switching to 64bit free
surfer would have fixed the issue. One observation though, it looks like you
are using the bert subject that was distributed with
Hi Alex
I think that
your design is very simple and so will be to use our lme tools. There is an
example of a mass-univariate analysis on the wiki at
http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics.
However, the analysis there is much more complex (because of the more complex
dat
Thanks, Doug
That was quite helpful, and I have just extracted the mean timeseries from one
of my parcellations. I just wanted to note a discrepancy between the
mri_segstats output and what is indicated in the mri_segstats --help output.
According to the program help:
--avgwf textfile
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