Hi Luis
sorry, the BA stuff is almost at the very end so you will need to run
pretty much everything. We are down to 8 hours or so on modern multi-core
CPUs (and even faster than that with 4-8 threads)
cheers
Bruce
On Tue, 22 Dec 2015, Luis
Fernado Silva Castro de Araújo wrote:
Do I have
you have to do the whole thing
On 12/21/2015 06:09 PM, Luis Fernado Silva Castro de Araújo wrote:
> Do I have to run recon-all entirely in order to extract volume for a
> few Brodmann's areas? Or is there a way of optimizing the process by
> striping it of any unneeded calculations?
>
> It is ta
can you cut and paste the error into the email rather than sending a
jpeg? Your image cut off the most important part
On 12/14/2015 09:54 PM, nellie wrote:
>
> Hi Freesurfer experts,
>
> When I tried to use *"Generate Stats Data Tables*" in QDEC, some
> errors came out. The related screenshot i
Can you run the command below outside of qdec and send us the error it
prints to the terminal?
asegstats2table --common-segs --meas volume --tablefile
/mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
--statsfile=aseg.stats --subjects 100307 101006 1
Do I have to run recon-all entirely in order to extract volume for a few
Brodmann's areas? Or is there a way of optimizing the process by striping
it of any unneeded calculations?
It is taking 21h to analyze one subject.
Best,
luis
2015-12-22 9:44 GMT+11:00 Douglas N Greve :
> If you're doing a
what server did you upload it to? What is the name of the file? Make
sure to include the entire output folder, not just the input files
On 12/21/2015 03:33 PM, Fengji Geng wrote:
> Hi Bruce,
>
> I have uploaded all the data to the server. The command that I run is
> 'recon-all -all -s $s -hippoc
If you're doing anatomical analysis, then FSFAST is not needed (nor its
directly structure). If you have an input anatomical volume in any
format, then just run
recon-all -s yoursubjectname -all -i inputfile
inputfile can include img but be warned that img does not have
information about head
Dear Douglas,
It's an anatomical analysis. Perhaps I misunderstood the requirement for
setting up the directories in the FSFAST for the recon-all command.
If that is the case, it is then a matter of converting my img files into
mgz and run recon-all on them, am I right?
Does the command recon-al
why did you not use fscalc, eg,
fscalc var.mgh -sqrt -o stderr.mgh
On 12/21/2015 03:04 PM, John Anderson wrote:
> Thanks Doug,
> I used the command "mris_calc gammavar.mgh sqrt" and the output was:
> _"Saving result to 'out.mgz' (type = MGH _)"
> *Then* I ran the command "mris_calc out.mgz stat
no way to help without more info.
On 12/21/2015 01:10 PM, Sabrina Yu wrote:
> When I try to load the overlay in freeview, it crashes immediately. Any
> thoughts on why this happens?
>
> Thanks
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> on behal
Sorry for the delay. Answers below
On 12/21/2015 03:58 PM, Woo, Jonghye wrote:
> Dear Doug,
>
> I have following questions: I posted the question but no one answered it.
>
> 1. What is the best way to convert annotation to the segmentation mask
> (volume)?
mri_label2vol. Specify the annotation wi
Hi Bruce,
I have uploaded all the data to the server. The command that I run is
'recon-all -all -s $s -hippocampal-subfields-T1T2 $s/T2/*.mgz T1T2'.
It would be great if you could keep us updated on how the fixing is going.
Thanks!
--
Hi Sabrina
you need to tell us what you did the caused the crash. What was the
command line? How did you try to load it?
cheers
Bruce
On Mon, 21 Dec 2015, Sabrina Yu
wrote:
> When I try to load the overlay in freeview, it crashes immediately. Any
> thoughts on why this happens?
>
> Thanks
>
>
Thanks Doug,
I used the command "mris_calc gammavar.mgh sqrt" and the output was: "Saving result to 'out.mgz' (type = MGH )"
Then I ran the command "mris_calc out.mgz stats" and the output was :
Size [ 163842 ]
Min@(index) [ 0.00 (161385) ]
Max
it helps to see the error msg, but my guess is that you need to specify
an mgh file, not a txt file. This will give you the voxel-wise stderr,
not a standard error for the cluster (which does not make sense)
On 12/21/2015 02:38 PM, John Anderson wrote:
> Hi Doug,
> Given that the standard var
Hi Doug,
Given that the standard variance can be calculated using the command "mris_calc" and the flag "-sqrt" what is the correct command to do this calculation?
I tried:
mris_calc gammavar.mgz -sqrt output.txt but it didn't work. Kindly what I am doing wrong?
Bests,
John
Sent: Mon
Not sure. Zeke?
On 12/21/2015 02:13 PM, std...@virgilio.it wrote:
> yes and this is the error:
> mri_fdr
> dyld: Library not loaded: @executable_path/../lib/gcc/lib/libstdc++.6.
> dylib
>Referenced from: /Applications/freesurfer/bin/mri_fdr
>Reason: image not found
> Trace/BPT trap
>
>
>>
QDEC cannot but the information may be in the output folder. There
should be a file called gammavar.mgh. This will be the standard variance
(so take the square root)
On 12/21/2015 02:08 PM, John Anderson wrote:
> Thanks you very much Doug,
> Please one more question. Is there any way in Qdec to
yes and this is the error:
mri_fdr
dyld: Library not loaded: @executable_path/../lib/gcc/lib/libstdc++.6.
dylib
Referenced from: /Applications/freesurfer/bin/mri_fdr
Reason: image not found
Trace/BPT trap
>Messaggio originale
>Da: gr...@nmr.mgh.harvard.edu
>Data: 21-dic-2015 20.04
>A:
Thanks you very much Doug,
Please one more question. Is there any way in Qdec to get the stamdard error (SE) ?
Bests,
John
Sent: Monday, December 21, 2015 at 11:43 AM
From: "Douglas N Greve"
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Qdec visualization
The correction
have you tried changing the permission to be exectuable?
chmod a+x mri_fdr
On 12/21/2015 02:02 PM, std...@virgilio.it wrote:
> Thanks but permission denied persist.
>
>
>> Messaggio originale
>> Da: gr...@nmr.mgh.harvard.edu
>> Data: 21-dic-2015 17.33
>> A:
>> Ogg: Re: [Freesurfer] R: R:
Thanks but permission denied persist.
>Messaggio originale
>Da: gr...@nmr.mgh.harvard.edu
>Data: 21-dic-2015 17.33
>A:
>Ogg: Re: [Freesurfer] R: R: Re: R: Re: FDR in FS-FAST
>
>
>Try this version for mac
>ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_fdr.
osx
>
>Use m
When I try to load the overlay in freeview, it crashes immediately. Any
thoughts on why this happens?
Thanks
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N Greve
Sent: Monday, December 21, 2015 10:08 AM
To: freesurfer@nmr.mgh.harv
freeview or tksurfer. Load the relevant map as an overlay
On 12/21/2015 12:57 PM, Sabrina Yu wrote:
> Hello,
>
> Thank you for the very helpful replies! I have another quick question. Which
> commands would I use to generate images like the ones in Figure 1 (C)
> generated in the Salat paper
>
Hello,
Thank you for the very helpful replies! I have another quick question. Which
commands would I use to generate images like the ones in Figure 1 (C)
generated in the Salat paper
(http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)?
Thank you
Sabrina
__
Hello Freesurfer experts,
I am wondering if the new hippocampal subfields (HSF) module that will be
included in Freesurfer v. 6 would work with 1.5 Tesla data.
Upon reviewing the mail archives, I came across a thread
(https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35665.html)
Hi FS Experts
I want to get the total area from pia cortex, in order to normalize the
parcellations measure. In lh.aparc.statsfile on there is a line:
# Measure Cortex, WhiteSurfArea, White Surface Total Area, ** mm^2
>
I've looking for this topic in the lista and I found there is a way to ge
The correction for multiple comparisons is cluster-based. Each cluster
gets a single number. In the display, all the vertices get that same number.
On 12/18/2015 03:17 PM, John Anderson wrote:
> Hi Freesurfer experts,
> I am using Qdec in Freesurfer 5.3 to do some cortical thickness
> comparison
here you go. I put rh there too
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/lh.DKTatlas40.gcs
On 12/18/2015 05:29 PM, Schweren, LJS (med) wrote:
>
> No, it doesn’t exist (lh nor rh)
>
> Can I get it somewhere?
>
> *From:*freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesur
Try this version for mac
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_fdr.osx
Use mri_surfcluster (or mri_volcluster) to do the clustering
On 12/18/2015 05:11 PM, std...@virgilio.it wrote:
> I have run
> mri_fdr --help
> but I obtained this warning:
> /Applications/freesurf
You can use mri_segstats --i z.nii.gz --id 1 --slabel ...
On 12/20/2015 08:44 AM, std...@virgilio.it wrote:
> Hi list,
>
> I would like to extract the mean z-score from a roi.label in each
> subject after FS-FAST (rs-fMRI seed based).
> How can I do?
>
> Thanks
>
>
> Stefano
>
>
> ___
that link works for me. Can you try again?
On 12/20/2015 02:17 AM, Thục Trinh wrote:
> Hi FS experts,
>
> I'm working on my fMRI data using FSFAST v.6 tool. But the first step
> of Preproc-sess was failed with an error :" *ERROR: cannot find AFNI
> command 3dvolreg.afni ". *
> I found a thread t
Hi Fengji
hmmm, I don't remember ever seeing a core dump in mri-segstats before. If
you upload the entire subject dir (tarred and gzipped) to our ftp site we
will fix it.
cheers
Bruce
On Mon, 21 Dec 2015, Fengji Geng wrote:
Dear fs experts,
Could anybody help with the error we reported
Dear Freesurfer experts,
I just started using Freesurfer for performing MRI (T1)- group-based ROI
analysis and managed to go through the first recon-all processing stream and
making few manual edits. Then I followed first steps of the Qdec -procedure.
However, there is a separate section on ROI
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