Dear list,
I have a question about extracting global lgi values/hemisphere. I think I
have managed to do it correctly using :
mri_segstats --slabel subj lh $SUBJECTS_DIR/subj/label/lh.cortex --i
$SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats
(Please let me know if this is no
is the 2nd number you want. The first is for the
> medial wall (not interesting). You can have it report only for cortex by
> adding --id 1
>
> doug
>
>
> On 11/13/2013 11:45 AM, Anna Jonsson wrote:
> > Dear list,
> >
> > I have a question about extracting glo
>
> On 11/13/2013 12:04 PM, Anna Jonsson wrote:
>
>> Thank you very much. By second I assume you mean second row? And out of
>> the values on the second row it must be the value 2.9472? Is it headed by
>> Area_mm2 or Mean? And what are the units?
>>
>> Thanks a
Dear list members,
I was wondering where in the Freesurfer output the information on which
freesurfer version has been used to process scans is located? eg
recon-all.log?
Thank you,
Kind Wishes,
Anna
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t;
> --parc aparc.pial_lgi
>
> doug
>
>
>
> On 11/14/2013 11:27 AM, Anna Jonsson wrote:
>
>> Thank you. Can I then use
>> aparcstats2table --subjects --hemi lh --meas thickness --parc
>> lh.aparc.pial_lgi.stats --tablefile aparc_lgi_lh.txt to get a
Dear Freesurfer experts,
I want to know if possible when doing longitudinal stream to put subjects
with only one time-point through the processing (eg base and long runs) in
order to subsequently use with the Matlab lme tools? Or better is to leave
them out and only do those with 2+ times?
Thank
s other subjects, with a cross sectional,
> -base and a -long step:
>
> recon-all -all -s -i path_to_tp1_dcm
>
> recon-all -base -tp -all
>
> recon-all -long -all
>
>
> Best, Martin
>
>
> On 02/18/2014 04:58 AM, Anna Jonsson wrote:
>
> Dear Freesu
Dear group,
If I want conduct gyrification analyses on the long runs that have been
through the longitudinal stream, do I just perform the "normal" baseline
command on the .long data?
thank you,
kind wishes
Anna
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> On Mar 15, 2014, at 10:04 AM, Anna Jonsson wrote:
>
> Dear group,
>
> If I want conduct gyrification analyses on the long runs that have been
> through the longitudinal stream, do I just perform the "normal" baseline
> comma
Hi I would like get a mean sulcal folding value per hemisphere and roi
data. I have two questions:
Is possible do sulcal depth analysis using qdec?
And
What is the exact command to pass to mris_anatomical_stats to get a mean
sulcal depth value /per hemisphere? I have tried some few variations wi
, and use
> that as kind of the definition of the transition from gyral to sulcal. We
> can add a switch to mris_inflate to inhibit this behavior if you want I
> suppose.
>
> cheers
> Bruce
> On Wed, 30 Apr 2014, Anna Jonsson wrote:
>
> > Hi I would like get a mean sulc
Dear group,
when using the qdec gui interface, I was wondering where the "button" or
the likes is to change the estimation from its standard doss to dods
(different osnet, different slope). I believe I can do this somewhere on
the qdec gui without changing to mri_glmfit?
__
On Mon, May 5, 2014 at 8:39 PM, Douglas N Greve
wrote:
>
> DOSS is not working in QDEC. It should be disabled in 5.3
> doug
>
> On 05/05/2014 09:39 AM, Anna Jonsson wrote:
> > Dear group,
> >
> > when using the qdec gui interface, I was wondering where the "
Hi,
I would like to make my freesurfer longitudinal qdec table for the to use
in the lme matlab tools. However, does the fsid need to refer to the
longitidunally derived subject; eg XXX.long, or the cross-sectionally
derived subject, eg XXX. Im not sure based on the specification online.
Kind Reg
---- Original message
> From: Anna Jonsson
> Date:06/04/2014 7:22 AM (GMT-05:00)
> To: Freesurfer support list
> Subject: [Freesurfer] free-surfer longitudinal Qdec table
>
> Hi,
>
> I would like to make my freesurfer longitudinal qdec table for the to use
> in t
in qdec format (with a
> fsid-base as second column. It would then use the longitudinally processed
> results, which is what you want , both for lme and 2 stage model.
> Best Martin
>
>
> Sent via my smartphone, please excuse brevity.
>
> Original message ----
rmat (with a
>> fsid-base as second column. It would then use the longitudinally processed
>> results, which is what you want , both for lme and 2 stage model.
>> Best Martin
>>
>>
>> Sent via my smartphone, please excuse brevity.
>>
>> Origina
c flag and it uses the .long.base file names).
>
> Best, Martin
>
>
> On Jun 24, 2014, at 5:23 PM, Anna Jonsson wrote:
>
> Thank you. I just another question about the fsid groupings for the qdec
> table for lme. If in the qdec I specify only the fisid (eg nt the
> lo
I also have this problem now. did this query ever resolve?
On Wed, Jun 4, 2014 at 10:55 PM, Qijing Yu wrote:
> Hello FreeSufers,
>
> I ran several analyses in qdec, and now have problem visualize previous
> analyses results...which sounds dumb... Please let me know if you have any
> ideas.
>
>
Dear group, I now have error loading my qdec table into qdec, for this error
fsid column:1
Number of factors: 8
Number of subjects: 168
ERROR: QdecSubject::GetContinuousFactor failure: could not find factor
name: age_demeaned for subject XXX
However those 5 of those "factors" are contini
hi, i never recieved answer for this problem...any ideas?
On Tue, Jul 8, 2014 at 11:13 AM, Anna Jonsson wrote:
> Dear group, I now have error loading my qdec table into qdec, for this
> error
>
> fsid column:1
> Number of factors: 8
> Number of subjects: 168
&g
:28 PM, Martin Reuter
wrote:
> Hi Anna,
>
> no, you would still do:
>
> recon-all -long tpid baseid -localGI
>
> just not use the '-all'.
>
> Best, Martin
>
>
>
>
> On 03/26/2014 11:12 AM, Anna Jonsson wrote:
>
> thank you. But if the
Dear group,
Is there a way to create a prefrontal cortex label in fresurfer? if so,
please tell me the exact steps to do so, I am very confused.
Thank you,
Anna
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> labels into an annotation or use mri_merge_label to merge them into a
> single label. All you have to do is decide with labels define prefontal
> doug
>
>
> On 10/23/2014 10:25 AM, Anna Jonsson wrote:
> > Dear group,
> >
> > Is there a way to create a prefrontal
hi, anyone can help with this?
On Tue, Nov 4, 2014 at 4:43 PM, Douglas N Greve
wrote:
> I don't know. Maybe someone else can weigh in.
> doug
>
> On 11/04/2014 07:38 AM, Anna Jonsson wrote:
> > thank you. which labels are normally included as prefrontal cortex for
hi, I have tried to make prefrotnal cortex label by doing first
mri_annotation2label --subject "$subject" --hemi rh --outdir
"$subject"/label
mri_mergelabels -i lh.caudalanteriorcingulate.label -i
lh.caudalmiddlefrontal.label -i lh.lateralorbitofrontal.label -i
lh.medialorbitofrontal.label -
could not read label file (null)
On Mon, Nov 24, 2014 at 4:56 PM, Douglas N Greve
wrote:
> What is the full terminal output and error msg?
>
> On 11/21/2014 04:14 AM, Anna Jonsson wrote:
> > hi, I have tried to make prefrotnal cortex label by doing first
> >
> >
&
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