Hi list, this error is still occurring:
mri_convert $SUBJECTS_DIR/subj/mri/MRS_MASK.nii.gz
$SUBJECTS_DIR//subj/mri/MRS_MASK.mgz
fcseed-config -segid 1 -seg $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz -fsd
rest -mean -cfg MRS_MASK.config
fcseed-sess -s -cfg MRS_MASK.config
During
fcseed-sess -s subj
Dear Freesurfer experts,
I know this has been an ongoing topic in the mailing list – however I would
like to raise the issue one more time. In the choice between doss and dods
– I usually check if there is a significant interaction and if so my choice
is dods.
As I understand it you do not recomm
Dear FreeSurfers,
I'm about to analyze cortical thickness in monozygotic twins discordant for
certain expertise. The within-pair similarities in brain morphology are
striking (e.g. twin1 x twin2 intracranial volume correlation r=.99) and you
could easily play a memory game with the images. None
Dear Douglas,
Thank you for response. To clarify, I need to find out where in the lGI
scripts zcat is being called so that I can change the code to use
something like gunzip.
Best, Derek
Derek Sayre Andrews, MSc
PhD Candidate
The Sackler Institute for
Dear FreeSurfer support team,
It appears that ‘zcat’ appears in line 126 of the load.mgh script, I have
changed this to gzcat which appears to have solved the issue.
Again, thank you for your support. It is very appreciated!
Best, Derek
Derek Sayre
Dear Heidi,
maybe there is a problem with your long.qdec.table.dat file? It is used
to create the .long. file names and obviously that
filename is wrong (containing two .long. in it). Make sure that the
first column is only the cross sectional id and the second one is the
base id, so in your
Hi Oerjan,
yes, MZ twins are very similar (InfoAd: are you familiar with our
BrainPrint NeuroImaging paper where we compare MZ and DZ brain shapes:
http://www.sciencedirect.com/science/article/pii/S1053811915000476
http://reuter.mit.edu/blue/papers/wachinger-brainprint15/wachinger-brainprint15.
Heidi,
first: you probably need to keep the .nii in the table for now
(depending on how your cross sectional directories are really named?).
If they have the .nii extension, you need to do the same in the qdec table.
If down the road the extension creates problems, it will be very
complicate
Ah, I see. But what do the 27307 rows represent and why are there 6 values per
row?
Thanks,
Afsana
__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 261
Hi freesurfers,
Following recon-all I have a collection of folders inside the subject folder.
Inside the folder "mri" I have collection of files:
1. What is the differnce between the file "orig.mgz" and the file "norm.mgz" ?
2. Why the voxel dimentions are differnt? (i.e In norm.mgz the vox
load_mgh.m and load_nifti.m in $FREESURFER_HOME/matlab
On 11/04/2015 06:33 AM, Andrews, Derek wrote:
> Dear Douglas,
>
> Thank you for response. To clarify, I need to find out where in the lGI
> scripts zcat is being called so that I can change the code to use
> something like gunzip.
>
> Best, De
First, when running fcseed-config, don't give it the full path, just the
path relative to subject/mri (in this case only MRS_MASK.mgz)
However, I don't think that is the problem. Please run
fcseed-sess -debug -s -cfg MRS_MASK.config |& tee doug.log
and send me doug.log
On 11/04/2015 04:1
Hi List,
I am getting the following error when running recon-all lgi for local
gyrification index.
I have changed the script in matlab as we are using matlab 2013b as
mentioned in the previous thread.
I am attaching the script.
Please let me know what else to do.
Thanks Regards
Meenal Budhiraja
Ph
Not sure what is going on. can you find (from the log) the command it
runs just before that (something with mris_label_calc) and run it in a
terminal (with the SUBJECT_DIR set etc). It could be that it get's
confused by the .nii extension, but could also be something else.
Martin
On 11/04/2
Works perfectly! Thank you so much!
Heidi
On 11/3/15, 6:54 PM, "Douglas N Greve" wrote:
>
>In that case you can do something like
>fscalc lhfile.mgz add 1000 -o lhfile1000.mgz
>mri_mask lhfile1000.mgz lhfile.mgz lhfile1000.mgz
>
>This will add 1000 to the lhlabels. This will make the lh labels
>
Dear FreeSurfer Experts,
When I specify --measure pial_lgi, aparcstats2table says it’s an invalid option.
Could you please advise how I can obtain an individual’s pial_lgi value, give a
label?
Many thanks!
Daniel
___
Freesurfer mailing list
Freesurfer
It is done to fit inside the nifti format. You can just put 163842
columns because nifti only supports max 32k
On 11/04/2015 10:11 AM, Afzal, Afsana wrote:
> Ah, I see. But what do the 27307 rows represent and why are there 6 values
> per row?
>
> Thanks,
>
> Afsana
> ___
On 11/04/2015 10:22 AM, John Anderson wrote:
> Hi freesurfers,
> Following recon-all I have a collection of folders inside the subject
> folder.
> Inside the folder "mri" I have collection of files:
> 1. What is the differnce between the file "orig.mgz" and the file
> "norm.mgz" ?
norm has been
Hi Chaz, unfortunately version 5 does not support arbitrary slice
orders. It will be available in version 6.
doug
On 11/03/2015 06:27 PM, Gay,Charles Wysaw wrote:
> Hi -
>
> 1) I am trying to perform preprocessing steps on functional task data
> that was acquired on a Phillips scanner using an i
http://www.alzforum.org/jobs/postdoctoral-fellow-neuropsychologyclinical-neuroscienceimaging
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Descript
Hi all,
Found an answer here:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-March/036542.html
It works for me!
Best,
Daniel
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Daniel Yang
mailto:daniel.yj.y...@yale.edu>>
Reply-To: Freesurfer support list
mailto
Hi Ray
that sounds right. The way I visualize these is using nmovie (which I
think we include in our distribution) and flipping back and forth between
the different images showing the different surfaces/curv maps.
Which inaccuracy are you referring to?
cheers
Bruce
On Wed, 4 Nov 2015, Razli
Hi Dough,
in summary:
I have the MRS_MASK.mgz within $SUBJECTS_DIR/Control22/mri
thus, I have copy this file in fMRI directory (fMRI/Control22_FS) the
MRS_MASK.mgz
and run:
fcseed-config -segid 1 -seg Control22_FS/MRS_MASK.mgz -fsd rest -mean -
cfg MRS_MASK.config
fcseed-sess -s Control22_FS -cfg
Hi Bruce,
Thanks for reply. I thought after registering, the source surface's curvature
map should be very similar to the target one. I don't see that here. The
registered surface has pretty much the same curvature map only slightly shifted.
Am I missing something here?
Best
On Nov 4, 2015, at
Hi Ray
what version of FS are you using? Can you send me the output of the
command? The distance term will prevent the curvatures from deforming too
much. You can set it much smaller and see what happens if you want. There
may also be an area constraint. Trying using -parea 0 also (or somethin
Hi Elisabetta
I don't think that's an error, just a warning. That said, a defect with
38K vertices is awfully big, almost 1/4 of the surface, which usually means
something big is wrong (e.g. cerebellum or skull attached to the hemi). Can
you look at the orig.nofix or the inflated.nofix and see
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