Hi Eugenio,
I managed to get the subfield code process to run, my cluster wasn't using all the allotted RAM for the job, thank you for all the input. Can I ask how long it typically takes as it appears to have completed in about 30mins and gave me the left and right dirs
with the volume txts
Hi All,
I have created two ROIs from first time point Qdec group comparison. I need
to use this ROI labels to extract the thickness from tp1 and tp2 registered
to base (template) subjects(from longitudinal pipeline).
Would you please let me how can I convert the label from 1st time point
space to l
Hi Erik,
30 mins for a subject sounds correct. If the text files with the volumes are
there, and the segmentations look plausible, then everything should be fine.
One more thing: it the outputs are in specific directories, please note that we
changed the naming convention and structure of the o
Hi:
I want to do a longitudinal study between two time points of a patient... I
want to compare the volume of the hypocampii, white matter, etc... I did
the computation of both time points, I created the "base" image, and the
"long" ones... How can I analyze the aseg.stats files in each "long" fol
Hi:
For example: if I want to compare the volume of left hyppocampus in two
time points, could I compare the volume in aseg.stats file of both "long"
folders?...
Sincerely,
Gonzalo Rojas Costa
Gonzalo Rojas Costa
Advanced Medical Image Processing Laboratory
Depa
Hi Gonzalo,
yes, exactly, you only look at the *.long.* folders. Take a look at this
page:
http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics
specifically if you have 2 time points for all subjects, you can use the
tools for analyzing slopes:
http://surfer.nmr.mgh.harvard.edu/fs
Hi,
We ran our subjects through version 5.1, did a thorough quality check and
troubleshoot the data, and then re-ran our subjects through version 5.3 to
verify that our findings were consistent between versions.
We're running into an issue where we are not able to replicate our
subcortical findin
Hi Maia
that's surprising and a bit worrisome. It's been a while so I don't
remember the details of the differences between 5.1 and 5.3. Did you have
to edit the aseg in 5.1?
cheers
Bruce
On Wed, 27 May 2015, Maia
Pujara wrote:
Hi,
We ran our subjects through version 5.1, did a thorough
download this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg
and copy it to $FREESURFER_HOME/bin
doug
On 05/26/2015 01:40 PM, Park, Jung Mi wrote:
> Hello Freesurfer
>
> *mni152reg --s 0201JB-anat*
> *=> *mkdir: cannot create directory
>
> `/usr/pubsw/packages/f
Can you list the 3 stats files you are talking about? I can't quite
follow from below
doug
On 05/26/2015 02:21 PM, zal...@u.washington.edu wrote:
> Hello Freesurfer team,
>
> When generating the .stats files for grey matter volumetric data, this
> information appears in multiple places and I'm n
Hi Gabriella, sorry for the delay
On 05/22/2015 09:15 AM, Hirsch, Gabriella wrote:
>
> HI FS experts,
>
> I haven’t heard back and am still wrestling with these questions. Any
> takers?
>
> I’d really appreciate any thoughts at all if possible.
>
> Thanks,
>
> Gabriella
>
> *From:*Hirsch, Gabriel
don't know. Can you send the recon-all.log file?
doug
On 05/25/2015 07:13 PM, Anvi K Vora wrote:
> Hi Doug,
>
> That file does not exist, because none of the surf files got created
> from this pipeline. So there was an error before that?
>
> The mri files got created (partially) and what's there
This appears to be a problem with the 5.3 version of freeview. I think
there is a way to get a newer version. Perhaps Zeke can point it out.
doug
On 05/26/2015 08:30 AM, Robert Kraft wrote:
> Doug,
>
>
> Thanks for responding to my question about to a custom lookup table in
> freeview. My apolo
Sorry for the delay. You should just run recon-all on
$FSLDIR/data/standard/MNI152_T1_1mm.nii.gz
It will give you a wmparc.mgz which you can then use directly with the
FSL output
doug
On 05/26/2015 04:59 PM, Estephan J. Moana-Filho wrote:
> Sorry, I thought my original post would be somehow lin
Hello FreeSurfers,
I am trying to run a clusterwise correction following this link:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
I would like to use the permutation simulation instead of Z Monte Carlo. I
ran mri_glmfit-sim --help to get more information.
Following an exampl
You can download the newest version of freeview by following the
instruction for "Freeview dev version" on this page:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
Make sure you download the copy that goes which your version of
freesurfer as listed in your FREESURFER_HOME/build-stamp.txt f
Thanks for the response, Doug!
Yes, here is the error message I get when I try to keep one measure (e.g. ICV
or global volume) in QDEC. As I said earlier, when I keep BOTH measures (like
keeping both ICV and global volume as nuisance factors) in a simple thickness
analysis between two groups, t
Are you sure there is not any white space after the backslash (\)?
If so, Can you run it with --debug as the first option?
On 05/27/2015 03:39 PM, Mihaela Stefan wrote:
> Hello FreeSurfers,
>
> I am trying to run a clusterwise correction following this link:
> https://surfer.nmr.mgh.harvard.edu/
Can you send me
/media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd
On 05/27/2015 03:47 PM, Hirsch, Gabriella wrote:
> Thanks for the response, Doug!
>
> Yes, here is the error message I get when I try to keep one measure (e.g. ICV
> or global volume) in QDEC. As I said earlier,
Sure thing, see attached.
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: Wednesday, May 27, 2015 4:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re:
Use mri_label2label. Run it with --help to get more info
doug
On 05/27/2015 05:08 AM, amirhossein manzouri wrote:
> Hi All,
> I have created two ROIs from first time point Qdec group comparison. I
> need to use this ROI labels to extract the thickness from tp1 and tp2
> registered to base (templ
still not sure, can you send these files?
/media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat
/media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/lh-Diff-EB-control-Intercept-thickness.mat
On 05/27/2015 04:30 PM, Hirsch, Gabriel
Thanks! It seems that there was a white space. I ran the permutation
command but now I got another error:
ERROR: design matrix is not orthogonal, cannot be used with permutation.
If this something you really want to do, run with --perm-force
Wed May 27 16:27:50 EDT 2015
ERROR: cannot find any csd
Sure.
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: Wednesday, May 27, 2015 4:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FW: cor
Hmm, still can't replicate the error. Can you post this file to our
filedrop (see end of msg for url)
/media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh
On 05/27/2015 04:40 PM, Hirsch, Gabriella wrote:
> Sure.
>
> From: freesurfer-boun...@nmr
Done. I wasn't sure if I had to put an email address for the recipient so I
put yours. Let me know if you figure it out! :) Thanks so much.
Gabriella
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N
Hi,
I have two groups and two time points (pre and post). I want to investigate
group*time interactions in an fMRI task taken at both time points.
I have run all the subjects through first level FEAT analyses in FSL as
well as the longitudinal Freesurfer pipeline.
I'm thinking of registering the
Right, strictly speaking, permutationis for orthogonal design matrices
only, which is not the case when you have a covariate. There was a
recent paper by Anderson Winkler "Permutation Inference for the General
Linear Model" in NI in which he goes over various permutation methods
for non-orthogo
Oh, sorry, this is not a problem with mri_glmfit as I had thought. It is
a problem with qdec itself on your data. I'm not sure what to tell you
because I can't debug it without your data (and maybe not even then).
You can use mri_glmfit directly.
doug
On 05/27/2015 04:49 PM, Hirsch, Gabriella w
Yes, it seems to be a qdec issue since mri_glmfit works by itself even without
demeaning the larger values of ICV. Thanks anyway.
One unrelated questions since I have you here; does FS produce a "total" or
"global" cortical surface area file along the lines of TotalGrayVol? I'm
looking for the
Hi Mike,
I doubt the 2-stage-model scripts will work for you. They were designed
for structural analysis.
But you can make use of the within-subject template space to do you fmri
analysis (map all fmri results there and do all within-subject
comparisons in that space before going across subjec
There should be one in aseg.stats.
On 05/27/2015 05:45 PM, Hirsch, Gabriella wrote:
> Yes, it seems to be a qdec issue since mri_glmfit works by itself even
> without demeaning the larger values of ICV. Thanks anyway.
>
> One unrelated questions since I have you here; does FS produce a "total" or
you can also do a paired analysis (search the wiki)
doug
On 05/27/2015 05:51 PM, Martin Reuter wrote:
> Hi Mike,
>
> I doubt the 2-stage-model scripts will work for you. They were
> designed for structural analysis.
> But you can make use of the within-subject template space to do you
> fmri ana
Hi Freesurfer Experts,
I have installed the dev version to test recon-alls on some subjects, but I
am running into the following error at the transformation stage. See below
for the error message:
/Applications/freesurfer6/bin/talairach_avi
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm --a
Hi FS Experts,
When I tried to segment the subfields using the Dev version on subjects
that have been previously processed with v5.3, I get the following error:
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Current Stamp: freesurfer-Darwin-m
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