You can inflate it more with something like
mris_inflate -dist .01 -f .001 -no-save-sulc 20 lh.smoothwm lh.inflated
20 is the number of iterations (default is 15) so play with that number
On 08/13/2014 11:25 AM, angela.fav...@unipd.it wrote:
> Hi Doug,
> a further question: my final symmetric
Hi Doug,
a further question: my final symmetric atlas seems to be not inflated
enough, but still have important sulcations.
Do I have to perform further iterations (myatlas.i4, myatlas.i5 )
until the resulting volume is good enough? Or which is the correct method
(other than performing asymmetr
thank you!
> sorry, I should have given you a new make_average_volume.
>
> you can get it from here
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_volume
>
>
> On 08/11/2014 07:52 AM, angela.fav...@unipd.it wrote:
>> Hi Doug, I am having a problem with the last ste
sorry, I should have given you a new make_average_volume.
you can get it from here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_volume
On 08/11/2014 07:52 AM, angela.fav...@unipd.it wrote:
> Hi Doug, I am having a problem with the last step of building my own
> sym
Oh! it works now!
thank you thank you thank you
Angela
> when you run make_average_subject, you will still need the --lh
> doug
>
> On 07/29/2014 06:07 PM, angela.fav...@unipd.it wrote:
>> ftp
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface
>> Connected to su
when you run make_average_subject, you will still need the --lh
doug
On 07/29/2014 06:07 PM, angela.fav...@unipd.it wrote:
> ftp
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface
> Connected to surfer.nmr.mgh.harvard.edu.
> 220-This is the Martinos Center Anonymo
ftp
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface
Connected to surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this site
220-shows implicit consent to our Acceptable Use Policy outlined at
220-http://www.nmr.mgh.harvard.
can you send the full terminal output
On 07/29/2014 06:00 PM, angela.fav...@unipd.it wrote:
> Hi Doug,
> unfortunately the same error message appear... it looks for
> rh.fsaverage_sym.sphere.reg
>
>
> #@# Making rh registration template -
> /Users/angelafavaro/Desktop/risonanze/studyfr
Hi Doug,
unfortunately the same error message appear... it looks for
rh.fsaverage_sym.sphere.reg
#@# Making rh registration template -
/Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1
mris_make_template -norot -annot aparc rh fsaverage_sym.sphere.reg subj001
subj001/xhemi su
Copy this file into $FREESURFER_HOME/bin (make a backup of the existing one)
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface
let me know if that works
doug
On 07/29/2014 05:37 PM, angela.fav...@unipd.it wrote:
> I am using 5.3
>
> make_average_subject --out mya
I am using 5.3
make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg
--subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol
--template-only --lh
make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg
--subjects subj001 subj002 subj003 subj004 sub
Is that all it prints out? What version of FS are you using?
On 07/29/2014 05:26 PM, angela.fav...@unipd.it wrote:
> ERROR: Flag --lh unrecognized.
>
>> Try adding --lh to the make_average_subject command line. Let me know if
>> that works and I'll change the docs
>> doug
>>
>>
>> On 07/29/2014
ERROR: Flag --lh unrecognized.
>
> Try adding --lh to the make_average_subject command line. Let me know if
> that works and I'll change the docs
> doug
>
>
> On 07/29/2014 05:13 PM, angela.fav...@unipd.it wrote:
>> Hi Doug, this the command and output (here with only five subjects).
>> thank you!
Try adding --lh to the make_average_subject command line. Let me know if
that works and I'll change the docs
doug
On 07/29/2014 05:13 PM, angela.fav...@unipd.it wrote:
> Hi Doug, this the command and output (here with only five subjects).
> thank you!
>
> make_average_subject --out myatlas.i1 -
Hi Doug, this the command and output (here with only five subjects).
thank you!
make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg
--subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol
--template-only
make_average_surface --out myatlas.i1 --surf-reg fsaverage_s
What is the command line that is failing and what is the full terminal
output?
doug
On 07/29/2014 05:55 AM, angela.fav...@unipd.it wrote:
> Hi all,
> I am now working with the 5.3 version and performing interhemispheric
> registration (building my own atlas)
>
> after running for all subjects:
Hi all,
I am now working with the 5.3 version and performing interhemispheric
registration (building my own atlas)
after running for all subjects:
xhemireg --s subj001
surfreg --s subj001 --t fsaverage_sym --lh
surfreg --s subj001 --t fsaverage_sym --xhemi --lh
I have tried first iteration, b
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