[Freesurfer] Fwd: V1 and V2 labels valid with clinical populations?

[krista kelly]

Just wanted to pose this question again to the Freesurfer community:

Can anyone provide any advice on how to justify using the V1, V2 labels in
FreeSurfer in clinical populations without also collecting functional
retinotopy data?

Thanks!
Krista

-- Forwarded message --
From: krista kelly 
Date: Wed, Jun 18, 2014 at 4:51 PM
Subject: Re: [Freesurfer] V1 and V2 labels valid with clinical populations?
To: Freesurfer support list 


OK thanks. I see a lot of pubs using these labels. Can anyone provide any
advice on how to justify using these labels in clinical populations without
also collecting functional retinotopy data?


On Wed, Jun 18, 2014 at 4:13 PM, Bruce Fischl 
wrote:

> Hi Krista
>
> I don't think we have any idea. The labels are based purely on anatomy, but
> whether those areas keep their functional specification we have no idea.
>
> let us know if you find out though!
> Bruce
> On Wed, 18 Jun 2014, krista kelly wrote:
>
> > Does anyone know of any support (i.e. articles/data) suggesting that the
> V1
> > and V2 labels automatically created in the Freesurfer pipeline,
> especially
> > when looking at surface area/gyrification, are valid to use with clinical
> > populations? In particular, visually deprived populations?
> > Thanks!
> > Krista
> >
> >
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>
>
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[Freesurfer] Compiling data from lobesStrict

[krista kelly]

Hi all,

I'm trying to extract cortical thickness data from each lobe per
participant. Here are the commands I used so far:

1) create annotation file for lobes: mri_annotation2label --subject $s
--hemi lh --lobesStrict lh.lobesStrict.annot

2) extract lobe labels: mri_annotation2label --subject $s --hemi lh
--annotation lobesStrict --outdir $s/label

3) create stats file for each lobe per participant: mris_anatomical_stats
-a $s/label/lh.lobesStrict.annot -b -f $s/stats/lh.lobesStrict.stats

PROBLEM: I'm stuck now on how to compile all of the data into one file.
I've tried:

aparcstats2table --subjects  --parc lobesStrict.annot --hemi
lh –meas thickness --tablefile lh.lobesStrict.thickness.stats.txt

I've also tried:

asegstats2table --subjects  --subdir=stats --statsfile
lh.lobesStrict --tablefile lh.lobesStrict.thickness.stats.txt

None of these work. Can someone please tell me what I'm doing wrong?

Thanks!
Krista
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Re: [Freesurfer] V1 and V2 labels valid with clinical populations?

[krista kelly]

OK thanks. I see a lot of pubs using these labels. Can anyone provide any
advice on how to justify using these labels in clinical populations without
also collecting functional retinotopy data?


On Wed, Jun 18, 2014 at 4:13 PM, Bruce Fischl 
wrote:

> Hi Krista
>
> I don't think we have any idea. The labels are based purely on anatomy, but
> whether those areas keep their functional specification we have no idea.
>
> let us know if you find out though!
> Bruce
> On Wed, 18 Jun 2014, krista kelly wrote:
>
> > Does anyone know of any support (i.e. articles/data) suggesting that the
> V1
> > and V2 labels automatically created in the Freesurfer pipeline,
> especially
> > when looking at surface area/gyrification, are valid to use with clinical
> > populations? In particular, visually deprived populations?
> > Thanks!
> > Krista
> >
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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[Freesurfer] V1 and V2 labels valid with clinical populations?

[krista kelly]

Does anyone know of any support (i.e. articles/data) suggesting that the V1
and V2 labels automatically created in the Freesurfer pipeline, especially
when looking at surface area/gyrification, are valid to use with clinical
populations? In particular, visually deprived populations?

Thanks!
Krista
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] extract pial_lgi from v1.thresh labels

[krista kelly]

Thanks Doug! That fixed it. But now I have two numbers in each file, which
do I use (see also attached file)?

ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max
Range  1 0 124241 81007.3 Seg 2.7306 0.6613 1.4985 4.4779 2.9795  2 1
3540 2225.6 Seg0001 2.4966 0.3254 2.0502 3.0296 0.9794










On Wed, Mar 5, 2014 at 5:07 PM, Douglas N Greve
wrote:

>
> Sorry, I gave you some bad advice. Only use --label-thresh with labels
> that have a statistic that is non-zero (this is the last column of the
> label file). Eg, in lh.V1.thresh.label, the stat is always 0 (but it is
> non-zero in lh.V1.label). The stat is the probability that the vertex is in
> the label, so you can choose the threshold based on that. The
> lh.V1.thresh.label is for when the stat is the max for V1 relative to the
> other labels (eg, V2). If you select thresh=.5, you may miss places where
> V1 is the most likely but still less than .5. I would probably use
> lh.V1.thresh.label (and then do not spec --label-thresh)
>
> doug
>
>
>
> On 03/05/2014 03:40 PM, krista kelly wrote:
>
>> Thanks Doug! I did that and it worked, but now here's another problem:
>> the values that I obtained for V1, V2, and cortex for each subject are all
>> the same. For example, BV20 left hemisphere values for V1, V2, and cortex
>> are all 2.7241 (same thing happens for the right hemisphere). Maybe I can
>> tell you what I did step by step to see  if you can find where I went wrong.
>>
>> First, I did a for loop to run mri_segstats for each participant for each
>> label per hemisphere (here is an example of V1):
>>
>> foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31
>> BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08
>> MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) <>
>> mri_segstats --label-thresh .5 --slabel $s lh
>> $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i
>> $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum 
>> $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats
>>  <>
>> end <>
>>
>> for left V2 I ran:
>>
>> foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31
>> BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08
>> MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) <>
>> mri_segstats --label-thresh .5 --slabel $s lh
>> $SUBJECTS_DIR/$s/label/lh.V2.thresh.label --i
>> $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum 
>> $SUBJECTS_DIR/$s/stats/lh.V2.thresh.label.LGI.stats
>>  <>
>> end <>
>>
>> and for left cortex I ran:
>> foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31
>> BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08
>> MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) <>
>> mri_segstats --label-thresh .5 --slabel $s lh 
>> $SUBJECTS_DIR/$s/label/lh.cortex
>> --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.
>> cortex.LGI.stats
>> end <>
>>
>>
>> This is where the problem must be occurring since all files created
>> during these commands show the same files per hemisphere. I've attached
>> three files created during mri_segstats (left V1, V2, cortex.stats) for one
>> participant. I've also attached files created during asegstats2table to
>> show how all values are the same for each label for all participants (V1,
>> V2, cortex.LGI.txt).
>>
>> If anyone has any insight into the problem, that would be great!
>>
>> Best,
>> Krista
>>
>>
>> On Wed, Mar 5, 2014 at 1:54 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>>
>> use asegstats2table (I know, it's confusing:)
>> doug
>>
>>
>>
>> On 03/05/2014 01:42 PM, krista kelly wrote:
>>
>> Hi again,
>>
>> My apologies for the barrage of emails! I was able to do
>> mri_segstats on V1 labels for pial_lgi using the following:
>>
>> mri_segstats --label-thresh .5 --slabel $s lh
>> $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i
>> $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
>> $SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats
>>
>> However, now I'm having trouble with bringing all of the data
>> into one table using aparcstats2table. I found online how to
>> get the data for aparc annotation
>> (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/
>

Re: [Freesurfer] extract pial_lgi from v1.thresh labels

[krista kelly]

Thanks Doug! I did that and it worked, but now here's another problem: the
values that I obtained for V1, V2, and cortex for each subject are all the
same. For example, BV20 left hemisphere values for V1, V2, and cortex are
all 2.7241 (same thing happens for the right hemisphere). Maybe I can tell
you what I did step by step to see  if you can find where I went wrong.

First, I did a for loop to run mri_segstats for each participant for each
label per hemisphere (here is an example of V1):

foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32
BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09
MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) <>
mri_segstats --label-thresh .5 --slabel $s lh
$SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i
$SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
$SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats  <>
end <>

for left V2 I ran:

foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32
BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09
MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) <>
mri_segstats --label-thresh .5 --slabel $s lh
$SUBJECTS_DIR/$s/label/lh.V2.thresh.label --i
$SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
$SUBJECTS_DIR/$s/stats/lh.V2.thresh.label.LGI.stats  <>
end <>

and for left cortex I ran:
foreach s (BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28 BV29 BV30 BV31 BV32
BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44 BV47 MB07 MB08 MB09
MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 MB19 MB20) <>
mri_segstats --label-thresh .5 --slabel $s lh
$SUBJECTS_DIR/$s/label/lh.cortex --i $SUBJECTS_DIR/$s/surf/lh.pial_lgi
--sum $SUBJECTS_DIR/$s/stats/lh.cortex.LGI.stats
end <>


This is where the problem must be occurring since all files created during
these commands show the same files per hemisphere. I've attached three
files created during mri_segstats (left V1, V2, cortex.stats) for one
participant. I've also attached files created during asegstats2table to
show how all values are the same for each label for all participants (V1,
V2, cortex.LGI.txt).

If anyone has any insight into the problem, that would be great!

Best,
Krista


On Wed, Mar 5, 2014 at 1:54 PM, Douglas N Greve
wrote:

>
> use asegstats2table (I know, it's confusing:)
> doug
>
>
>
> On 03/05/2014 01:42 PM, krista kelly wrote:
>
>> Hi again,
>>
>> My apologies for the barrage of emails! I was able to do mri_segstats on
>> V1 labels for pial_lgi using the following:
>>
>> mri_segstats --label-thresh .5 --slabel $s lh
>> $SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i
>> $SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum $SUBJECTS_DIR/$s/stats/lh.V1.
>> thresh.label.LGI.stats
>>
>> However, now I'm having trouble with bringing all of the data into one
>> table using aparcstats2table. I found online how to get the data for aparc
>> annotation (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/
>> 2013-September/033069.html) and tried to adapt to the labels. Here is
>> what I've tried:
>>
>> aparcstats2table --subjects BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28
>> BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44
>> BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 --hemi lh
>> --meas thickness --parc V1.thresh.label.LGI --tablefile
>> lh.V1.thresh.label.LGI.txt
>>
>> I get the following output when I do this:
>>
>> SUBJECTS_DIR : /Applications/freesurfer/subjects
>> Parsing the .stats files
>> Traceback (most recent call last):
>>   File "/Applications/freesurfer/bin/aparcstats2table", line 371, in
>> 
>> parc_measure_map = parsed.parse(options.meas)
>>   File "/Applications/freesurfer/bin/fsutils.py", line 207, in parse
>> val = float(strlist[self.measure_column_map[measure]])
>> ValueError: could not convert string to float: Seg
>>
>> I've attached an example of the file created during mri_segstats in case
>> that helps.
>>
>> Thanks!
>> Krista
>>
>>
>> On Wed, Mar 5, 2014 at 1:21 PM, krista kelly 
>> > krista.kell...@gmail.com>> wrote:
>>
>> Perfect, it works thanks!
>>
>>
>> On Wed, Mar 5, 2014 at 11:35 AM, Douglas N Greve
>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>> sorry, it is --slabel
>> btw, there is documentation. If you run it without options it
>> gives you a list of arguments as well as examples
>> doug
>>
>> On 03/05/2014 11:32 AM, krista kelly wrote:
>>
>> Thanks Doug, but when I try this I ge

Re: [Freesurfer] extract pial_lgi from v1.thresh labels

[krista kelly]

Hi again,

My apologies for the barrage of emails! I was able to do mri_segstats on V1
labels for pial_lgi using the following:

mri_segstats --label-thresh .5 --slabel $s lh
$SUBJECTS_DIR/$s/label/lh.V1.thresh.label --i
$SUBJECTS_DIR/$s/surf/lh.pial_lgi --sum
$SUBJECTS_DIR/$s/stats/lh.V1.thresh.label.LGI.stats

However, now I'm having trouble with bringing all of the data into one
table using aparcstats2table. I found online how to get the data for aparc
annotation (
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033069.html)
and tried to adapt to the labels. Here is what I've tried:

aparcstats2table --subjects BV20 BV21 BV22 BV23 BV24 BV25 BV26 BV27 BV28
BV29 BV30 BV31 BV32 BV33 BV34 BV35 BV36 BV37 BV38 BV39 BV40 BV41 BV43 BV44
BV47 MB07 MB08 MB09 MB10 MB11 MB12 MB13 MB14 MB15 MB16 MB17 MB18 --hemi lh
--meas thickness --parc V1.thresh.label.LGI --tablefile
lh.V1.thresh.label.LGI.txt

I get the following output when I do this:

SUBJECTS_DIR : /Applications/freesurfer/subjects
Parsing the .stats files
Traceback (most recent call last):
  File "/Applications/freesurfer/bin/aparcstats2table", line 371, in

parc_measure_map = parsed.parse(options.meas)
  File "/Applications/freesurfer/bin/fsutils.py", line 207, in parse
val = float(strlist[self.measure_column_map[measure]])
ValueError: could not convert string to float: Seg

I've attached an example of the file created during mri_segstats in case
that helps.

Thanks!
Krista


On Wed, Mar 5, 2014 at 1:21 PM, krista kelly wrote:

> Perfect, it works thanks!
>
>
> On Wed, Mar 5, 2014 at 11:35 AM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> sorry, it is --slabel
>> btw, there is documentation. If you run it without options it gives you a
>> list of arguments as well as examples
>> doug
>>
>> On 03/05/2014 11:32 AM, krista kelly wrote:
>>
>>> Thanks Doug, but when I try this I get the following error: Option
>>> --label unknown
>>>
>>>
>>> On Wed, Mar 5, 2014 at 11:21 AM, Douglas N Greve <
>>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>>
>>>
>>> try
>>> mri_segstats --label-thresh .5 --label BV20 lh V1.thresh.label --i
>>> $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats
>>>
>>> On 03/05/2014 11:15 AM, krista kelly wrote:
>>> > Hello,
>>> >
>>> > I would like to extract the pial_lgi data from Freesurfer's
>>> V1.thresh
>>> > labels but can't quite figure it out. I've tried adapting the
>>> commands
>>> > from the LGI Freesurfer tutorial as such:
>>> >
>>> > mri_segstats --label-thresh BV20 lh V1.thresh.label --i
>>> > $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats
>>> >
>>> > I've also tried
>>> >
>>> > mris_anatomical_stats -l lh.V1.thresh.label -f
>>> > BV20/stats/lh.V1.thresh.label.stats BV20 lh pial_lgi
>>> >
>>> > but I've had no luck with either.
>>> >
>>> > I would appreciate any help!
>>> >
>>> > Thanks,
>>> > Krista
>>> >
>>> >
>>> > ___
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>
>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>>> Phone Number: 617-724-2358 
>>> Fax: 617-726-7422 
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>>>
>>> Outgoing:
>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh.
>>> harvard.edu>
>>>
>>> https://mail.nmr.mgh.harvard.edu/mailma

Re: [Freesurfer] extract pial_lgi from v1.thresh labels

[krista kelly]

Perfect, it works thanks!


On Wed, Mar 5, 2014 at 11:35 AM, Douglas N Greve
wrote:

> sorry, it is --slabel
> btw, there is documentation. If you run it without options it gives you a
> list of arguments as well as examples
> doug
>
> On 03/05/2014 11:32 AM, krista kelly wrote:
>
>> Thanks Doug, but when I try this I get the following error: Option
>> --label unknown
>>
>>
>> On Wed, Mar 5, 2014 at 11:21 AM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>>
>> try
>> mri_segstats --label-thresh .5 --label BV20 lh V1.thresh.label --i
>> $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats
>>
>> On 03/05/2014 11:15 AM, krista kelly wrote:
>> > Hello,
>> >
>> > I would like to extract the pial_lgi data from Freesurfer's
>> V1.thresh
>> > labels but can't quite figure it out. I've tried adapting the
>> commands
>> > from the LGI Freesurfer tutorial as such:
>> >
>> > mri_segstats --label-thresh BV20 lh V1.thresh.label --i
>> > $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats
>> >
>> > I've also tried
>> >
>> > mris_anatomical_stats -l lh.V1.thresh.label -f
>> > BV20/stats/lh.V1.thresh.label.stats BV20 lh pial_lgi
>> >
>> > but I've had no luck with either.
>> >
>> > I would appreciate any help!
>> >
>> > Thanks,
>> > Krista
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>> Phone Number: 617-724-2358 
>> Fax: 617-726-7422 
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>>
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu
>> >
>>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to
>> whom it is
>> addressed. If you believe this e-mail was sent to you in error and
>> the e-mail
>> contains patient information, please contact the Partners
>> Compliance HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to
>> you in error
>> but does not contain patient information, please contact the
>> sender and properly
>> dispose of the e-mail.
>>
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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>
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Re: [Freesurfer] extract pial_lgi from v1.thresh labels

[krista kelly]

Thanks Doug, but when I try this I get the following error: Option --label
unknown


On Wed, Mar 5, 2014 at 11:21 AM, Douglas N Greve
wrote:

>
> try
> mri_segstats --label-thresh .5 --label BV20 lh V1.thresh.label --i
> $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats
>
> On 03/05/2014 11:15 AM, krista kelly wrote:
> > Hello,
> >
> > I would like to extract the pial_lgi data from Freesurfer's V1.thresh
> > labels but can't quite figure it out. I've tried adapting the commands
> > from the LGI Freesurfer tutorial as such:
> >
> > mri_segstats --label-thresh BV20 lh V1.thresh.label --i
> > $SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats
> >
> > I've also tried
> >
> > mris_anatomical_stats -l lh.V1.thresh.label -f
> > BV20/stats/lh.V1.thresh.label.stats BV20 lh pial_lgi
> >
> > but I've had no luck with either.
> >
> > I would appreciate any help!
> >
> > Thanks,
> > Krista
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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[Freesurfer] extract pial_lgi from v1.thresh labels

[krista kelly]

Hello,

I would like to extract the pial_lgi data from Freesurfer's V1.thresh
labels but can't quite figure it out. I've tried adapting the commands from
the LGI Freesurfer tutorial as such:

mri_segstats --label-thresh BV20 lh V1.thresh.label --i
$SUBJECTS_DIR/BV20/surf/lh.pial_lgi --sum lh.V1.thresh.label.stats

I've also tried

mris_anatomical_stats -l lh.V1.thresh.label -f
BV20/stats/lh.V1.thresh.label.stats BV20 lh pial_lgi

but I've had no luck with either.

I would appreciate any help!

Thanks,
Krista
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Re: [Freesurfer] LGI in Qdec

[krista kelly]

Hi Marie,

It appears that the problem was the program that I was using to create the
. Qdecrc file. I was using Text Wrangler. I switched to TextMate and the
problem has been resolved.

Thanks so much for your help!
Krista


On Tue, Mar 4, 2014 at 8:27 PM, Marie Schaer  wrote:

>
>  Hi Krista,
>
>  Did you verify that your changes to .Qdecrc were properly saved? As long
> as the command more ~/.Qdecrc doesn't give you a line with MEASURE1 =
> pial_lgi, then you'll not have it in qdec menu. And version should not be
> an issue. How do you edit the .Qdecrc file? Did you check to see whether
> opening qdec had any effect on the line that you added (by running the
> command more ~/.Qdecrc before and after opening qdec)?
>
>  I need you to explain me a bit more how you did, otherwise it's
> difficult for me to help you.
>
>  Marie
>
>
>  On Mar 4, 2014, at 5:20 PM, krista kelly 
>  wrote:
>
>  Hi Marie,
>
>  Thanks for the the response. I've done that a few times and still, the
> lgi option does not come up in qdec as a measure. Could it be that I'm
> using an outdated version of Qdec? My freesurfer v is 5.3 so unless I need
> to update qdec on its own, I don't think that this is the problem. Any
> other ideas?
>
>  Best,
> Krista
>
>
> On Fri, Feb 28, 2014 at 4:16 PM, Marie Schaer wrote:
>
>>
>>  Hi Krista,
>>
>>  You need to add the following line in your .Qdecrc:
>>  MEASURE1 = pial_lgi
>>  and save the change.
>>
>>  I don't think it matters where you add it, I have it before all the
>> Qdec lines.
>>
>>  Then start qdec again, it should work. If not, check again the .Qdecrc
>> file, and look whether starting qdec erases the added line.
>>
>>  Let me know,
>>
>>  Marie
>>
>>  On Feb 28, 2014, at 1:09 PM, krista kelly 
>>   wrote:
>>
>>  Hi Marie,
>>
>>  The ?h.pial_lgi.fwhm?.fsaverage.mgh files in the surf folder are there. Here
>> is the output when I run more ~/.Qdecrc:
>>
>>  # This file is automatically generated by the application
>> # If you change any lines or add new lines, note that all
>> # coments and empty lines will be deleted. Every line has
>> # to be in format:
>> # key = value
>> #
>> Qdec1\Dialogs\ExitApplication = 0
>> Qdec1\Dialogs\SendErrorLog = 0
>> Qdec1\Geometry\MainPanelSize = 375
>> Qdec1\Geometry\MainPanelVisibility = 1
>> Qdec1\Geometry\SaveUserInterfaceGeometry = 1
>> Qdec1\Geometry\SecondaryPanelSize = 250
>> Qdec1\Geometry\SecondaryPanelVisibility = 0
>> Qdec1\Geometry\ViewPanelPosition = Right
>> Qdec1\Geometry\WindowGeometry = 900x700+787+1
>> Qdec1\MRU\File00 =
>> /Applications/freesurfer/subjects/qdec/qdec.tableNoBV45orBV46.dat
>> Qdec1\MRU\File00Cmd = LoadDataTable
>> Qdec1\RunTime\MostRecentVersionLaunched = 1.4
>> Qdec1\RunTime\PrintTargetDPI = 100.00
>> Qdec1\RunTime\ShowBalloonHelp = 1
>> Qdec1\RunTime\ShowSplashScreen = 1
>> Qdec1\RunTime\ToolbarFlatButtons = 1
>> Qdec1\RunTime\ToolbarFlatFrame = 1
>>
>>
>>  Thanks!
>> Krista
>>
>>
>> On Wed, Feb 26, 2014 at 7:12 PM, Marie Schaer wrote:
>>
>>>
>>>  Hi Krista,
>>>
>>>  Can you please run:
>>> more ~/.Qdecrc
>>> and copy paste the output for me?
>>>
>>>  The "rm: No match" issue in the qcache is not a problem, it's
>>> independent from the issue of listing lGI in the qdec menu. Even with the
>>> no match output in the qcache command, all the files should have been
>>> created properly (you can check that you have some files named
>>> ?h.pial_lgi.fwhm?.fsaverage.mgh in the surf folder of one of your subject
>>> if you want to be sure.
>>>
>>>  Let me know,
>>>
>>>  Marie
>>>
>>>  On Feb 25, 2014, at 6:55 PM, krista kelly 
>>> wrote:
>>>
>>>  Hi Marie,
>>>
>>>  I have tried adding the .Qdecrc file into the home folder as well but
>>> that does not work. The lgi measure is not appearing in the dropdown menu
>>> in the design tab in Qdec. Further, when I ran recon-all -qcache -measure
>>> pial_lgi, there were error messages saying 'rm: No match', although the
>>> -qcache exited without errors. Could this be the problem? If not, does
>>> anyone have any ideas?
>>>
>>>  Thanks!
>>> Krista
>>>
>>>
>>> On Mon, Feb 24, 2014 at 4:29 PM, Marie Schaer wrote

Re: [Freesurfer] LGI in Qdec

[krista kelly]

Hi Marie,

Thanks for the the response. I've done that a few times and still, the lgi
option does not come up in qdec as a measure. Could it be that I'm using an
outdated version of Qdec? My freesurfer v is 5.3 so unless I need to update
qdec on its own, I don't think that this is the problem. Any other ideas?

Best,
Krista


On Fri, Feb 28, 2014 at 4:16 PM, Marie Schaer  wrote:

>
>  Hi Krista,
>
>  You need to add the following line in your .Qdecrc:
>  MEASURE1 = pial_lgi
>  and save the change.
>
>  I don't think it matters where you add it, I have it before all the Qdec
> lines.
>
>  Then start qdec again, it should work. If not, check again the .Qdecrc
> file, and look whether starting qdec erases the added line.
>
>  Let me know,
>
>  Marie
>
>  On Feb 28, 2014, at 1:09 PM, krista kelly 
>  wrote:
>
>  Hi Marie,
>
>  The ?h.pial_lgi.fwhm?.fsaverage.mgh files in the surf folder are there. Here
> is the output when I run more ~/.Qdecrc:
>
>  # This file is automatically generated by the application
> # If you change any lines or add new lines, note that all
> # coments and empty lines will be deleted. Every line has
> # to be in format:
> # key = value
> #
> Qdec1\Dialogs\ExitApplication = 0
> Qdec1\Dialogs\SendErrorLog = 0
> Qdec1\Geometry\MainPanelSize = 375
> Qdec1\Geometry\MainPanelVisibility = 1
> Qdec1\Geometry\SaveUserInterfaceGeometry = 1
> Qdec1\Geometry\SecondaryPanelSize = 250
> Qdec1\Geometry\SecondaryPanelVisibility = 0
> Qdec1\Geometry\ViewPanelPosition = Right
> Qdec1\Geometry\WindowGeometry = 900x700+787+1
> Qdec1\MRU\File00 =
> /Applications/freesurfer/subjects/qdec/qdec.tableNoBV45orBV46.dat
> Qdec1\MRU\File00Cmd = LoadDataTable
> Qdec1\RunTime\MostRecentVersionLaunched = 1.4
> Qdec1\RunTime\PrintTargetDPI = 100.00
> Qdec1\RunTime\ShowBalloonHelp = 1
> Qdec1\RunTime\ShowSplashScreen = 1
> Qdec1\RunTime\ToolbarFlatButtons = 1
> Qdec1\RunTime\ToolbarFlatFrame = 1
>
>
>  Thanks!
> Krista
>
>
> On Wed, Feb 26, 2014 at 7:12 PM, Marie Schaer wrote:
>
>>
>>  Hi Krista,
>>
>>  Can you please run:
>> more ~/.Qdecrc
>> and copy paste the output for me?
>>
>>  The "rm: No match" issue in the qcache is not a problem, it's
>> independent from the issue of listing lGI in the qdec menu. Even with the
>> no match output in the qcache command, all the files should have been
>> created properly (you can check that you have some files named
>> ?h.pial_lgi.fwhm?.fsaverage.mgh in the surf folder of one of your subject
>> if you want to be sure.
>>
>>  Let me know,
>>
>>  Marie
>>
>>  On Feb 25, 2014, at 6:55 PM, krista kelly 
>> wrote:
>>
>>  Hi Marie,
>>
>>  I have tried adding the .Qdecrc file into the home folder as well but
>> that does not work. The lgi measure is not appearing in the dropdown menu
>> in the design tab in Qdec. Further, when I ran recon-all -qcache -measure
>> pial_lgi, there were error messages saying 'rm: No match', although the
>> -qcache exited without errors. Could this be the problem? If not, does
>> anyone have any ideas?
>>
>>  Thanks!
>> Krista
>>
>>
>> On Mon, Feb 24, 2014 at 4:29 PM, Marie Schaer wrote:
>>
>>>
>>> Hi Krista,
>>>
>>> Can you be more specific about what is not coming up? If lGI not listed
>>> in the menu of qdec, look at the following post:
>>> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33427.html
>>>
>>> Otherwise can you describe more precisely the issue?
>>>
>>> Best,
>>>
>>> Marie
>>>
>>> On Feb 24, 2014, at 1:21 PM, krista kelly 
>>>   wrote:
>>>
>>> > Hello,
>>> >
>>> > I followed instructions on how to incorporate the lgi_pial measure
>>> into QDec, however, it's not coming up when I go to choose this as a
>>> measure. I ran recon-all -s my_subject_id -qcache -measure pial_lgi and
>>> created a Qdecrc file in my $SUBJECTS_DIR directory. Does anyone have any
>>> insight as to why this may be occurring?
>>> >
>>> > Thanks,
>>> > Krista
>>>  > ___
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> >
>>> >
>>> > The information in this e-mail is intended only for the person to whom
>>> it is
>>> > addressed. If

Re: [Freesurfer] LGI in Qdec

[krista kelly]

Hi Marie,

The ?h.pial_lgi.fwhm?.fsaverage.mgh files in the surf folder are there. Here
is the output when I run more ~/.Qdecrc:

# This file is automatically generated by the application
# If you change any lines or add new lines, note that all
# coments and empty lines will be deleted. Every line has
# to be in format:
# key = value
#
Qdec1\Dialogs\ExitApplication = 0
Qdec1\Dialogs\SendErrorLog = 0
Qdec1\Geometry\MainPanelSize = 375
Qdec1\Geometry\MainPanelVisibility = 1
Qdec1\Geometry\SaveUserInterfaceGeometry = 1
Qdec1\Geometry\SecondaryPanelSize = 250
Qdec1\Geometry\SecondaryPanelVisibility = 0
Qdec1\Geometry\ViewPanelPosition = Right
Qdec1\Geometry\WindowGeometry = 900x700+787+1
Qdec1\MRU\File00 =
/Applications/freesurfer/subjects/qdec/qdec.tableNoBV45orBV46.dat
Qdec1\MRU\File00Cmd = LoadDataTable
Qdec1\RunTime\MostRecentVersionLaunched = 1.4
Qdec1\RunTime\PrintTargetDPI = 100.00
Qdec1\RunTime\ShowBalloonHelp = 1
Qdec1\RunTime\ShowSplashScreen = 1
Qdec1\RunTime\ToolbarFlatButtons = 1
Qdec1\RunTime\ToolbarFlatFrame = 1


Thanks!
Krista


On Wed, Feb 26, 2014 at 7:12 PM, Marie Schaer  wrote:

>
>  Hi Krista,
>
>  Can you please run:
> more ~/.Qdecrc
> and copy paste the output for me?
>
>  The "rm: No match" issue in the qcache is not a problem, it's
> independent from the issue of listing lGI in the qdec menu. Even with the
> no match output in the qcache command, all the files should have been
> created properly (you can check that you have some files named
> ?h.pial_lgi.fwhm?.fsaverage.mgh in the surf folder of one of your subject
> if you want to be sure.
>
>  Let me know,
>
>  Marie
>
>  On Feb 25, 2014, at 6:55 PM, krista kelly 
> wrote:
>
>  Hi Marie,
>
>  I have tried adding the .Qdecrc file into the home folder as well but
> that does not work. The lgi measure is not appearing in the dropdown menu
> in the design tab in Qdec. Further, when I ran recon-all -qcache -measure
> pial_lgi, there were error messages saying 'rm: No match', although the
> -qcache exited without errors. Could this be the problem? If not, does
> anyone have any ideas?
>
>  Thanks!
> Krista
>
>
> On Mon, Feb 24, 2014 at 4:29 PM, Marie Schaer wrote:
>
>>
>> Hi Krista,
>>
>> Can you be more specific about what is not coming up? If lGI not listed
>> in the menu of qdec, look at the following post:
>> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33427.html
>>
>> Otherwise can you describe more precisely the issue?
>>
>> Best,
>>
>> Marie
>>
>> On Feb 24, 2014, at 1:21 PM, krista kelly 
>>   wrote:
>>
>> > Hello,
>> >
>> > I followed instructions on how to incorporate the lgi_pial measure into
>> QDec, however, it's not coming up when I go to choose this as a measure. I
>> ran recon-all -s my_subject_id -qcache -measure pial_lgi and created a
>> Qdecrc file in my $SUBJECTS_DIR directory. Does anyone have any insight as
>> to why this may be occurring?
>> >
>> > Thanks,
>> > Krista
>>  > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> > contains patient information, please contact the Partners Compliance
>> HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> > but does not contain patient information, please contact the sender and
>> properly
>> > dispose of the e-mail.
>>
>>
>
>
___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] LGI in Qdec

[krista kelly]

Hi Marie,

I have tried adding the .Qdecrc file into the home folder as well but that
does not work. The lgi measure is not appearing in the dropdown menu in the
design tab in Qdec. Further, when I ran recon-all -qcache -measure
pial_lgi, there were error messages saying 'rm: No match', although the
-qcache exited without errors. Could this be the problem? If not, does
anyone have any ideas?

Thanks!
Krista


On Mon, Feb 24, 2014 at 4:29 PM, Marie Schaer  wrote:

>
> Hi Krista,
>
> Can you be more specific about what is not coming up? If lGI not listed in
> the menu of qdec, look at the following post:
> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33427.html
>
> Otherwise can you describe more precisely the issue?
>
> Best,
>
> Marie
>
> On Feb 24, 2014, at 1:21 PM, krista kelly 
>  wrote:
>
> > Hello,
> >
> > I followed instructions on how to incorporate the lgi_pial measure into
> QDec, however, it's not coming up when I go to choose this as a measure. I
> ran recon-all -s my_subject_id -qcache -measure pial_lgi and created a
> Qdecrc file in my $SUBJECTS_DIR directory. Does anyone have any insight as
> to why this may be occurring?
> >
> > Thanks,
> > Krista
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the person to whom
> it is
> > addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> > contains patient information, please contact the Partners Compliance
> HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> > but does not contain patient information, please contact the sender and
> properly
> > dispose of the e-mail.
>
>
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] LGI in Qdec

[krista kelly]

Hello,

I followed instructions on how to incorporate the lgi_pial measure into
QDec, however, it's not coming up when I go to choose this as a measure. I
ran recon-all -s my_subject_id -qcache -measure pial_lgi and created a
Qdecrc file in my $SUBJECTS_DIR directory. Does anyone have any insight as
to why this may be occurring?

Thanks,
Krista
___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_surfcluster

[krista kelly]

Thanks Doug! I realize this doesn't do FDR but I've gotten the FDR
threshold from tksurfer and will use that as my -thmin.

One last thing, how would I view the results of mri_surfclluster in
tksurfer? Would I load the  ocn.mgh file? If so, I can't seem to find it.


On Thu, Jan 23, 2014 at 2:02 PM, Douglas N Greve
wrote:

> just add "--subject fsaverage_sym"
>
> btw, that command does not perform FDR
>
> doug
>
> On 01/23/2014 01:41 PM, krista kelly wrote:
> > Hi all,
> >
> > I have obtained laterality indices using xhemi analyses and would like
> > to use FDR instead of the mri_glmfit-sim suggested in the xhemi
> > instructions. I know to get the FDR threshold from tksurfer, but I
> > want to restrict the clusters to a certain cluster size. Based on a
> > previous thread (
> > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23866.html
> > ) I think this should be done using mri_surfcluster but I am having
> > trouble with the actual commands. I've tried this but it doesn't seem
> > to work:
> >
> > mri_surfcluster --in glm.lh.lh-rh.thickness.BV.LI.mgh --thmin 2.54
> > --ocn ocn.mgh --sum sum.dat --sign abs --minarea 20 --surf
> > fsaverage_sym --hemi lh
> >
> > the error = srcsubjid must be supplied
> >
> > If I'm performing this on a group file (not individual subject), what
> > would I even input as the subjid? Or do I have this totally wrong?
> >
> > Thanks!
> > Krista
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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[Freesurfer] mri_surfcluster

[krista kelly]

Hi all,

I have obtained laterality indices using xhemi analyses and would like to
use FDR instead of the mri_glmfit-sim suggested in the xhemi instructions.
I know to get the FDR threshold from tksurfer, but I want to restrict the
clusters to a certain cluster size. Based on a previous thread (
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23866.html )
I think this should be done using mri_surfcluster but I am having trouble
with the actual commands. I've tried this but it doesn't seem to work:

mri_surfcluster --in glm.lh.lh-rh.thickness.BV.LI.mgh --thmin 2.54 --ocn
ocn.mgh --sum sum.dat --sign abs --minarea 20 --surf fsaverage_sym --hemi
lh

the error = srcsubjid must be supplied

If I'm performing this on a group file (not individual subject), what would
I even input as the subjid? Or do I have this totally wrong?

Thanks!
Krista
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Fwd: xhemi correct for multiple comparisons

[krista kelly]

Hi Doug,

Sorry I should have specified BETWEEN groups analyses. I have two groups
(control, patient) and I wanted to see if the hemisphere asymmetries (or
laterality indices) differed between groups. Is there a way to do that?

Thanks for all you help!
Krista


On Mon, Jan 13, 2014 at 6:25 PM, Douglas N Greve
wrote:

>
> yes, it is just like a "normal" group analysis. You create a stack of LI
> maps, one for each subject, create an FSGD file, run mri_glmfit, then
> mri_glmfit-sim.
>
> doug
>
>
>
> On 01/13/2014 06:22 PM, krista kelly wrote:
> >
> > Just wanted to repost this in case anyone else can give some advice.
> > Thanks!
> >
> > Is there any way to analyze group differences with xhemi? I can get
> > the laterality indices per group, but I'd like to do a whole brain
> > analyses looking at group differences in laterality indices.
> >
> > Thanks,
> > Krista
> >
> >
> > On Tue, Dec 10, 2013 at 2:01 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> >
> > Yes, use the cache files. When "--cache" is used, the csdbase="cache"
> >
> > On 12/10/2013 12:20 PM, krista kelly wrote:
> > > Hi again,
> > >
> > > I've looked into mri_glmfit-sim --help to figure out which files I
> > > could overlay in tkurfer after correcting for multiple comparisons
> > > using the instructions for xhemi on the freesurfer wiki.
> > However, I do
> > > not see any of these files (csd.base...) in the glmdir/osgm
> > folder. I
> > > only see ones that begin with cache. Are these the files I
> > should
> > > be overlaying? Or should I be using different commands for my
> > analyses?
> > >
> > > here is the command line I used:
> > >
> > > mri_glmfit-sim --glmdir glm.lh.lh-rh.area.pial.sm05 \
> > > --cwpvalthresh .5 --cache 2 abs
> > >
> > > Prior to mri_glmfit, I conducted the "create a stack of subjects"
> > > using paired-diff-norm in place of paired-diff
> > >
> > > Ultimately, I want to look at hemisphere asymmetries (preferably in
> > > terms of laterality indices) in two different groups separately.
> > >
> > > I would also like to see if laterality indices differ between
> > groups.
> > > Is this possible?
> > >
> > > Thanks!
> > > Krista
> > >
> > >
> > > On Mon, Dec 9, 2013 at 4:00 PM, krista kelly
> >     mailto:krista.kell...@gmail.com>
> > > <mailto:krista.kell...@gmail.com
> > <mailto:krista.kell...@gmail.com>>> wrote:
> > >
> > > Great Thanks!
> > >
> > >
> > >
> > >
> > > On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve
> > >  > <mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
> > >
> > >
> > > On 12/09/2013 11:53 AM, krista kelly wrote:
> > > > Thanks Doug! I'll try that instead.
> > > >
> > > > Also, do you or anyone else happen to have the answers
> > to my
> > > other
> > > > questions (reposted below):
> > > >
> > > > 1) When viewing the results in tksurfer, which color
> > > represents "left
> > > > hemisphere is larger" and which represents "right
> > hemisphere
> > > is larger"?
> > > If you are just doing a simple interhemispheric
> > difference, then
> > > yellow/red will be left>right and blue left > > >
> > > > 2) I have no idea how to view the results in tksurfer
> > AFTER
> > > performing
> > > > the step of correcting for multiple comparisons. Any
> > > suggestions?
> > >
> > > If you run mri_glmfit-sim with --help you will see a list
> of
> > > output
> > > files with descriptions for each. Choose the one you
> > want and run
> > > tksurfer on it (eg, tksurfer fsaverage_sym lh inflated
&g

Re: [Freesurfer] V1.thresh

[krista kelly]

Thanks so much Louis! This was exactly what I was looking for. The Hinds et
al. (2009) paper also has this info.


On Thu, Jan 16, 2014 at 5:02 PM, Louis Nicholas Vinke <
vi...@nmr.mgh.harvard.edu> wrote:

> Hi Krista,
> I believe the v?.thresh labels are thresholded at p=0.8.  This threshold
> is based on comparisons of actual and predicted V1 boundary with an
> independent dataset.
>
> Relevant pub: https://surfer.nmr.mgh.harvard.edu/ftp/articles/
> hinds2008accurate.pdf
>
> -Louis
>
>
> On Thu, 16 Jan 2014, krista kelly wrote:
>
>  Hi all,
>> Can anyone provide information regarding how v1.thresh.label and
>> v2.thresh.label that are automatically implemented
>> in FreeSurfer are thresholded?
>>
>> Thanks!
>> Krista
>>
>>
>>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] V1.thresh

[krista kelly]

Hi all,

Can anyone provide information regarding how v1.thresh.label and
v2.thresh.label that are automatically implemented in FreeSurfer are
thresholded?

Thanks!
Krista
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Fwd: xhemi correct for multiple comparisons

[krista kelly]

Just wanted to repost this in case anyone else can give some advice. Thanks!

Is there any way to analyze group differences with xhemi? I can get the
laterality indices per group, but I'd like to do a whole brain analyses
looking at group differences in laterality indices.

Thanks,
Krista


On Tue, Dec 10, 2013 at 2:01 PM, Douglas N Greve
wrote:

>
> Yes, use the cache files. When "--cache" is used, the csdbase="cache"
>
> On 12/10/2013 12:20 PM, krista kelly wrote:
> > Hi again,
> >
> > I've looked into mri_glmfit-sim --help to figure out which files I
> > could overlay in tkurfer after correcting for multiple comparisons
> > using the instructions for xhemi on the freesurfer wiki. However, I do
> > not see any of these files (csd.base...) in the glmdir/osgm folder. I
> > only see ones that begin with cache. Are these the files I should
> > be overlaying? Or should I be using different commands for my analyses?
> >
> > here is the command line I used:
> >
> > mri_glmfit-sim --glmdir glm.lh.lh-rh.area.pial.sm05 \
> > --cwpvalthresh .5 --cache 2 abs
> >
> > Prior to mri_glmfit, I conducted the "create a stack of subjects"
> > using paired-diff-norm in place of paired-diff
> >
> > Ultimately, I want to look at hemisphere asymmetries (preferably in
> > terms of laterality indices) in two different groups separately.
> >
> > I would also like to see if laterality indices differ between groups.
> > Is this possible?
> >
> > Thanks!
> > Krista
> >
> >
> > On Mon, Dec 9, 2013 at 4:00 PM, krista kelly  > <mailto:krista.kell...@gmail.com>> wrote:
> >
> > Great Thanks!
> >
> >
> >
> >
> > On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>>
> wrote:
> >
> >
> > On 12/09/2013 11:53 AM, krista kelly wrote:
> > > Thanks Doug! I'll try that instead.
> > >
> > > Also, do you or anyone else happen to have the answers to my
> > other
> > > questions (reposted below):
> > >
> > > 1) When viewing the results in tksurfer, which color
> > represents "left
> > > hemisphere is larger" and which represents "right hemisphere
> > is larger"?
> > If you are just doing a simple interhemispheric difference, then
> > yellow/red will be left>right and blue left > >
> > > 2) I have no idea how to view the results in tksurfer AFTER
> > performing
> > > the step of correcting for multiple comparisons. Any
> > suggestions?
> >
> > If you run mri_glmfit-sim with --help you will see a list of
> > output
> > files with descriptions for each. Choose the one you want and run
> > tksurfer on it (eg, tksurfer fsaverage_sym lh inflated -aparc
> > -overlay
> > csdbase.sig.cluster.mgh )
> >
> > doug
> >
> > >
> > > Thanks!
> > > Krista
> > >
> > >
> > >
> > >
> > > On Mon, Dec 9, 2013 at 11:09 AM, Douglas N Greve
> > >  > <mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
> > >
> > > Run mris_preproc with --paired-diff-norm which will then
> > compute
> > >LI = (L-R)/(.5*(L+R))
> > > Note that some people use
> > >LI = (L-R)/(L+R)
> > > If that is what you want, then divide the mris_preproc
> > result by 2
> > >
> > > doug
> > >
> > > On 12/08/2013 08:45 PM, krista kelly wrote:
> > > > Hello,
> > > >
> > > > I'm analysing interhemispheric differences using
> > xhemi. I have
> > > > followed the instructions on the webpage with no
> > problems. I do
> > > have a
> > > > few questions though.
> > > >
> > > > 1) When viewing the results in tksurfer, which color
> > represents
> > > "left
> > 

Re: [Freesurfer] xhemi correct for multiple comparisons

[krista kelly]

great thanks Doug!

Is there any way to analyze group differences with xhemi? I can get the
laterality indices per group, but I'd like to do a whole brain analyses
looking at group differences in laterality indices.

Thanks,
Krista


On Tue, Dec 10, 2013 at 2:01 PM, Douglas N Greve
wrote:

>
> Yes, use the cache files. When "--cache" is used, the csdbase="cache"
>
> On 12/10/2013 12:20 PM, krista kelly wrote:
> > Hi again,
> >
> > I've looked into mri_glmfit-sim --help to figure out which files I
> > could overlay in tkurfer after correcting for multiple comparisons
> > using the instructions for xhemi on the freesurfer wiki. However, I do
> > not see any of these files (csd.base...) in the glmdir/osgm folder. I
> > only see ones that begin with cache. Are these the files I should
> > be overlaying? Or should I be using different commands for my analyses?
> >
> > here is the command line I used:
> >
> > mri_glmfit-sim --glmdir glm.lh.lh-rh.area.pial.sm05 \
> > --cwpvalthresh .5 --cache 2 abs
> >
> > Prior to mri_glmfit, I conducted the "create a stack of subjects"
> > using paired-diff-norm in place of paired-diff
> >
> > Ultimately, I want to look at hemisphere asymmetries (preferably in
> > terms of laterality indices) in two different groups separately.
> >
> > I would also like to see if laterality indices differ between groups.
> > Is this possible?
> >
> > Thanks!
> > Krista
> >
> >
> > On Mon, Dec 9, 2013 at 4:00 PM, krista kelly  > <mailto:krista.kell...@gmail.com>> wrote:
> >
> > Great Thanks!
> >
> >
> >
> >
> > On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>>
> wrote:
> >
> >
> > On 12/09/2013 11:53 AM, krista kelly wrote:
> > > Thanks Doug! I'll try that instead.
> > >
> > > Also, do you or anyone else happen to have the answers to my
> > other
> > > questions (reposted below):
> > >
> > > 1) When viewing the results in tksurfer, which color
> > represents "left
> > > hemisphere is larger" and which represents "right hemisphere
> > is larger"?
> > If you are just doing a simple interhemispheric difference, then
> > yellow/red will be left>right and blue left > >
> > > 2) I have no idea how to view the results in tksurfer AFTER
> > performing
> > > the step of correcting for multiple comparisons. Any
> > suggestions?
> >
> > If you run mri_glmfit-sim with --help you will see a list of
> > output
> > files with descriptions for each. Choose the one you want and run
> > tksurfer on it (eg, tksurfer fsaverage_sym lh inflated -aparc
> > -overlay
> > csdbase.sig.cluster.mgh )
> >
> > doug
> >
> > >
> > > Thanks!
> > > Krista
> > >
> > >
> > >
> > >
> > > On Mon, Dec 9, 2013 at 11:09 AM, Douglas N Greve
> > >  > <mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
> > >
> > > Run mris_preproc with --paired-diff-norm which will then
> > compute
> > >LI = (L-R)/(.5*(L+R))
> > > Note that some people use
> > >LI = (L-R)/(L+R)
> > > If that is what you want, then divide the mris_preproc
> > result by 2
> > >
> > > doug
> > >
> > > On 12/08/2013 08:45 PM, krista kelly wrote:
> > > > Hello,
> > > >
> > > > I'm analysing interhemispheric differences using
> > xhemi. I have
> > > > followed the instructions on the webpage with no
> > problems. I do
> > > have a
> > > > few questions though.
> > > >
> > > > 1) When viewing the results in tksurfer, which color
> > represents
> > > "left
> > > > hemisphere is larger" and which 

Re: [Freesurfer] xhemi correct for multiple comparisons

[krista kelly]

Hi again,

I've looked into mri_glmfit-sim --help to figure out which files I could
overlay in tkurfer after correcting for multiple comparisons using the
instructions for xhemi on the freesurfer wiki. However, I do not see any of
these files (csd.base...) in the glmdir/osgm folder. I only see ones that
begin with cache. Are these the files I should be overlaying? Or should
I be using different commands for my analyses?

here is the command line I used:

mri_glmfit-sim --glmdir glm.lh.lh-rh.area.pial.sm05 \
--cwpvalthresh .5 --cache 2 abs

Prior to mri_glmfit, I conducted the "create a stack of subjects" using
paired-diff-norm in place of paired-diff

Ultimately, I want to look at hemisphere asymmetries (preferably in terms
of laterality indices) in two different groups separately.

I would also like to see if laterality indices differ between groups. Is
this possible?

Thanks!
Krista


On Mon, Dec 9, 2013 at 4:00 PM, krista kelly wrote:

> Great Thanks!
>
>
>
>
> On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>>
>> On 12/09/2013 11:53 AM, krista kelly wrote:
>> > Thanks Doug! I'll try that instead.
>> >
>> > Also, do you or anyone else happen to have the answers to my other
>> > questions (reposted below):
>> >
>> > 1) When viewing the results in tksurfer, which color represents "left
>> > hemisphere is larger" and which represents "right hemisphere is larger"?
>> If you are just doing a simple interhemispheric difference, then
>> yellow/red will be left>right and blue left> >
>> > 2) I have no idea how to view the results in tksurfer AFTER performing
>> > the step of correcting for multiple comparisons. Any suggestions?
>>
>> If you run mri_glmfit-sim with --help you will see a list of output
>> files with descriptions for each. Choose the one you want and run
>> tksurfer on it (eg, tksurfer fsaverage_sym lh inflated -aparc -overlay
>> csdbase.sig.cluster.mgh )
>>
>> doug
>>
>> >
>> > Thanks!
>> > Krista
>> >
>> >
>> >
>> >
>> > On Mon, Dec 9, 2013 at 11:09 AM, Douglas N Greve
>> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>> >
>> > Run mris_preproc with --paired-diff-norm which will then compute
>> >LI = (L-R)/(.5*(L+R))
>> > Note that some people use
>> >LI = (L-R)/(L+R)
>> > If that is what you want, then divide the mris_preproc result by 2
>> >
>> > doug
>> >
>> > On 12/08/2013 08:45 PM, krista kelly wrote:
>> > > Hello,
>> > >
>> > > I'm analysing interhemispheric differences using xhemi. I have
>> > > followed the instructions on the webpage with no problems. I do
>> > have a
>> > > few questions though.
>> > >
>> > > 1) When viewing the results in tksurfer, which color represents
>> > "left
>> > > hemisphere is larger" and which represents "right hemisphere is
>> > larger"?
>> > >
>> > > 2) I have no idea how to view the results in tksurfer AFTER
>> > performing
>> > > the step of correcting for multiple comparisons. Any suggestions?
>> > >
>> > > 3) I've noticed from the archives that some people are performing
>> > > laterality indices. How would I calculate laterality indices?
>> > >
>> > > Thanks!
>> > > Krista
>> > >
>> > >
>> > >
>> > >
>> > > ___
>> > > Freesurfer mailing list
>> > > Freesurfer@nmr.mgh.harvard.edu
>> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> > --
>> > Douglas N. Greve, Ph.D.
>> > MGH-NMR Center
>> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
>> > Phone Number: 617-724-2358 
>> > Fax: 617-726-7422 
>> >
>> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> > 

[Freesurfer] mris_anatomical_stats error

[krista kelly]

Hi,

I'm trying to run mris_anatomical_stats to get cortical thickness from
labels for each participant but I keep getting the following error:

MRISread: file '/Applications/freesurfer/subjects/MB19/surf/lh.thickness'
has many more faces than vertices!
Probably trying to use a scalar data file as a surface!

Here is the command I'm using:

mris_anatomical_stats -l MB07/label/lh.V1.thresh.label -b -f
MB07/stats/lh.V1.thresh.thickness.stats MB07 lh thickness

I wasn't able to find a suitable solution from the archives. I used the
same command to get area.pial stats without any problems. Any help is
appreciated!

Krista
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] xhemi correct for multiple comparisons

[krista kelly]

Great Thanks!




On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve
wrote:

>
> On 12/09/2013 11:53 AM, krista kelly wrote:
> > Thanks Doug! I'll try that instead.
> >
> > Also, do you or anyone else happen to have the answers to my other
> > questions (reposted below):
> >
> > 1) When viewing the results in tksurfer, which color represents "left
> > hemisphere is larger" and which represents "right hemisphere is larger"?
> If you are just doing a simple interhemispheric difference, then
> yellow/red will be left>right and blue left >
> > 2) I have no idea how to view the results in tksurfer AFTER performing
> > the step of correcting for multiple comparisons. Any suggestions?
>
> If you run mri_glmfit-sim with --help you will see a list of output
> files with descriptions for each. Choose the one you want and run
> tksurfer on it (eg, tksurfer fsaverage_sym lh inflated -aparc -overlay
> csdbase.sig.cluster.mgh )
>
> doug
>
> >
> > Thanks!
> > Krista
> >
> >
> >
> >
> > On Mon, Dec 9, 2013 at 11:09 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > Run mris_preproc with --paired-diff-norm which will then compute
> >LI = (L-R)/(.5*(L+R))
> > Note that some people use
> >LI = (L-R)/(L+R)
> > If that is what you want, then divide the mris_preproc result by 2
> >
> > doug
> >
> > On 12/08/2013 08:45 PM, krista kelly wrote:
> > > Hello,
> > >
> > > I'm analysing interhemispheric differences using xhemi. I have
> > > followed the instructions on the webpage with no problems. I do
> > have a
> > > few questions though.
> > >
> > > 1) When viewing the results in tksurfer, which color represents
> > "left
> > > hemisphere is larger" and which represents "right hemisphere is
> > larger"?
> > >
> > > 2) I have no idea how to view the results in tksurfer AFTER
> > performing
> > > the step of correcting for multiple comparisons. Any suggestions?
> > >
> > > 3) I've noticed from the archives that some people are performing
> > > laterality indices. How would I calculate laterality indices?
> > >
> > > Thanks!
> > > Krista
> > >
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the person to
> > whom it is
> > addressed. If you believe this e-mail was sent to you in error and
> > the e-mail
> > contains patient information, please contact the Partners
> > Compliance HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to
> > you in error
> > but does not contain patient information, please contact the
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>

Re: [Freesurfer] xhemi correct for multiple comparisons

[krista kelly]

Thanks Doug! I'll try that instead.

Also, do you or anyone else happen to have the answers to my other
questions (reposted below):

1) When viewing the results in tksurfer, which color represents "left
hemisphere is larger" and which represents "right hemisphere is larger"?

2) I have no idea how to view the results in tksurfer AFTER performing the
step of correcting for multiple comparisons. Any suggestions?

Thanks!
Krista




On Mon, Dec 9, 2013 at 11:09 AM, Douglas N Greve
wrote:

> Run mris_preproc with --paired-diff-norm which will then compute
>LI = (L-R)/(.5*(L+R))
> Note that some people use
>LI = (L-R)/(L+R)
> If that is what you want, then divide the mris_preproc result by 2
>
> doug
>
> On 12/08/2013 08:45 PM, krista kelly wrote:
> > Hello,
> >
> > I'm analysing interhemispheric differences using xhemi. I have
> > followed the instructions on the webpage with no problems. I do have a
> > few questions though.
> >
> > 1) When viewing the results in tksurfer, which color represents "left
> > hemisphere is larger" and which represents "right hemisphere is larger"?
> >
> > 2) I have no idea how to view the results in tksurfer AFTER performing
> > the step of correcting for multiple comparisons. Any suggestions?
> >
> > 3) I've noticed from the archives that some people are performing
> > laterality indices. How would I calculate laterality indices?
> >
> > Thanks!
> > Krista
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
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> HelpLine at
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[Freesurfer] xhemi correct for multiple comparisons

[krista kelly]

Hello,

I'm analysing interhemispheric differences using xhemi. I have followed the
instructions on the webpage with no problems. I do have a few questions
though.

1) When viewing the results in tksurfer, which color represents "left
hemisphere is larger" and which represents "right hemisphere is larger"?

2) I have no idea how to view the results in tksurfer AFTER performing the
step of correcting for multiple comparisons. Any suggestions?

3) I've noticed from the archives that some people are performing
laterality indices. How would I calculate laterality indices?

Thanks!
Krista
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[Freesurfer] bad skull strip but pial and white matter borders ok

[krista kelly]

Hi,

I have one subject with a poor skull strip - much of the skull and neck are
left over. I have used one of the automated processes to remove the
problems areas and I now the skull strip is fine. If the talarairching,
pial and white matter borders, and labels were fine, do I need to rerun any
of the recon-all steps?

Thanks!
Krista
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Re: [Freesurfer] possible pial surface editing

[krista kelly]

Hi Gen,

I'm having the same problem right now with one participant where the pial
matter border doesn't extend enough out to the edge of the cortex. Did you
try adding control points as Ye suggested? If so, did it work?

Thanks!
Krista


On Tue, Sep 24, 2013 at 11:52 AM, ye tian  wrote:

> Dear Gen,
>
> Since nobody replied to this message, I say try adding control points on
> the white matter close to where the gray matter is missing.
>
> Good luck!
>
> Ye
>
>
> On Tue, Sep 17, 2013 at 9:44 PM, Gennan Chen wrote:
>
>>  Hi! All,
>>
>>
>>
>> We ran into a few cases which the wm matter surface is pretty decent but
>> pial surface did not go far enough to include all gray matter. Is there a
>> way to fix this?
>>
>>
>>
>> Gen
>>
>> --
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Re: [Freesurfer] Within group hemisphere comparison in QDec

[krista kelly]

Great thanks! I'll try that. I've also figured out that I can just add the
subjects into the brackets that say subject list. But I'll try your method
just in case I'm wrong. Thanks again!


On Tue, Dec 3, 2013 at 11:26 PM, Douglas Greve wrote:

>
> On 12/3/13 11:08 PM, krista kelly wrote:
>
> Great thanks Douglas! I'm glad that this is available, I wasn't too keen
> on using the 'flip the brain' method of looking for hemisphere asymmetries.
>
> Just a few questions regarding the first step - Apply an existing atlas
> (fsaverage_sym); this looks like a "for" loop, which I'm not great at
> figuring out. I would like to know how to actually do this.
>
>  It seems like I would need to give it a list of all my subjects so that
> it can go through each subject separately without me having to run each
> participant separately. Is that correct? If so, and I have 40 participants,
> I'll need to leave the computer for a few days to do this. Is that correct?
>
> Yes.
>
>
>  Lastly, how do I create the subject list? I tried just creating a list
> of my subjects using text mate and keeping it in the subjects folder, then
> using that in place of (subject list). This didn't work.
>
> You're half way there, just
> set subjectlist = `cat subjectlistfile`
> where subjectlistfile is the file that you created (which can be called
> anything)
> doug
>
>
>
>
>  Thanks again!
>
>
> On Sat, Nov 30, 2013 at 2:34 PM, Douglas Greve 
> wrote:
>
>>
>> yep, we have an existing stream complete with documentation and a
>> publication you can cite!
>> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
>>
>>
>>
>> On 11/30/13 12:59 PM, krista kelly wrote:
>>
>>  Hello,
>>
>>  I need to do a within group hemisphere comparison to see if there are
>> any hemisphere asymmetries in a patient group. I would like to do this in
>> QDec or if possible, somehow do it in freesurfer without using Qdec. I
>> asked this question two years ago and you mentioned that you were working
>> on this and it should be available soon. Has there been any progress?
>>
>>  Thanks!
>> Krista
>>
>>
>>  ___
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>>
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Re: [Freesurfer] Within group hemisphere comparison in QDec

[krista kelly]

Great thanks Douglas! I'm glad that this is available, I wasn't too keen on
using the 'flip the brain' method of looking for hemisphere asymmetries.

Just a few questions regarding the first step - Apply an existing atlas
(fsaverage_sym); this looks like a "for" loop, which I'm not great at
figuring out. I would like to know how to actually do this.

It seems like I would need to give it a list of all my subjects so that it
can go through each subject separately without me having to run each
participant separately. Is that correct? If so, and I have 40 participants,
I'll need to leave the computer for a few days to do this. Is that correct?

Lastly, how do I create the subject list? I tried just creating a list of
my subjects using text mate and keeping it in the subjects folder, then
using that in place of (subject list). This didn't work.

Thanks again!


On Sat, Nov 30, 2013 at 2:34 PM, Douglas Greve wrote:

>
> yep, we have an existing stream complete with documentation and a
> publication you can cite!
> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
>
>
>
> On 11/30/13 12:59 PM, krista kelly wrote:
>
> Hello,
>
>  I need to do a within group hemisphere comparison to see if there are
> any hemisphere asymmetries in a patient group. I would like to do this in
> QDec or if possible, somehow do it in freesurfer without using Qdec. I
> asked this question two years ago and you mentioned that you were working
> on this and it should be available soon. Has there been any progress?
>
>  Thanks!
> Krista
>
>
> ___
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>
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[Freesurfer] Within group hemisphere comparison in QDec

[krista kelly]

Hello,

I need to do a within group hemisphere comparison to see if there are any
hemisphere asymmetries in a patient group. I would like to do this in QDec
or if possible, somehow do it in freesurfer without using Qdec. I asked
this question two years ago and you mentioned that you were working on this
and it should be available soon. Has there been any progress?

Thanks!
Krista
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Re: [Freesurfer] .label versus .thresh.label

[krista kelly]

Ok great! Thanks for the quick responses, and for your help.

Best,
Krista


On Sun, Nov 17, 2013 at 1:26 PM, Bruce Fischl wrote:

> no, those are whole-brain parcellations so ever vertex is already assigned
> the most likely label for it
>
>
> cheers
> Bruce
> On Sun, 17 Nov 2013, krista kelly wrote:
>
>  Ok perfect. Just one last question, how would I use the thresholded option
>> for the annotations (i.e. aparc.DKTatlas40.annot, aparc2009s.annot) when
>> doing whole brain analyses?
>> Thanks!
>>
>>
>> On Sun, Nov 17, 2013 at 1:20 PM, Bruce Fischl > >
>> wrote:
>>   for most purposes, yes
>>   Bruce
>>   On Sun, 17 Nov 2013, krista kelly wrote:
>>
>> Great thanks Bruce! I'm assuming then that using the
>> thresh.label is the
>> best choice.
>>
>>
>> On Sun, Nov 17, 2013 at 12:50 PM, Bruce Fischl
>> 
>> wrote:
>>   Hi Krista
>>
>>   the unthresholded labels give every point that
>> has a non-zero
>>   probability of being in the label, no matter
>> how unlikely. The
>>   .thresh ones are thresholded to pick the most
>> likely vertices
>>   that give a label that is the right surface
>> area.
>>
>>   cheers
>>   Bruce
>>   On Sun, 17 Nov 2013, krista kelly wrote:
>>
>> Hi, I've just started using the newest
>> freesurfer v
>> 5.3 and I've noticed in
>> the labels folder that every .label has
>> a
>> thresh.label. When overlaying the
>> two, they can be quite different (for
>> example
>> MT.label is much larger than
>> MT.thresh.label) or quite similar
>> (V1.label is just
>> a tiny bit larger than
>> V1.thresh.label). What is the difference
>> between the
>> two and which is best
>> to use?
>> Thanks!
>> Krista
>>
>>
>>
>>
>> The information in this e-mail is intended only for
>> the person to whom
>> it is
>> addressed. If you believe this e-mail was sent to
>> you in error and the
>> e-mail
>> contains patient information, please contact the
>> Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the
>> e-mail was sent to you
>> in error
>> but does not contain patient information, please
>> contact the sender
>> and properly
>> dispose of the e-mail.
>>
>>
>>
>>
>>
>>
>>
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Re: [Freesurfer] .label versus .thresh.label

[krista kelly]

Ok perfect. Just one last question, how would I use the thresholded option
for the annotations (i.e. aparc.DKTatlas40.annot, aparc2009s.annot) when
doing whole brain analyses?

Thanks!


On Sun, Nov 17, 2013 at 1:20 PM, Bruce Fischl wrote:

> for most purposes, yes
>
> Bruce
> On Sun, 17 Nov 2013, krista kelly wrote:
>
>  Great thanks Bruce! I'm assuming then that using the thresh.label is the
>> best choice.
>>
>>
>> On Sun, Nov 17, 2013 at 12:50 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   Hi Krista
>>
>>   the unthresholded labels give every point that has a non-zero
>>   probability of being in the label, no matter how unlikely. The
>>   .thresh ones are thresholded to pick the most likely vertices
>>   that give a label that is the right surface area.
>>
>>   cheers
>>   Bruce
>>   On Sun, 17 Nov 2013, krista kelly wrote:
>>
>> Hi, I've just started using the newest freesurfer v
>> 5.3 and I've noticed in
>> the labels folder that every .label has a
>> thresh.label. When overlaying the
>> two, they can be quite different (for example
>> MT.label is much larger than
>> MT.thresh.label) or quite similar (V1.label is just
>> a tiny bit larger than
>> V1.thresh.label). What is the difference between the
>> two and which is best
>> to use?
>> Thanks!
>> Krista
>>
>>
>>
>>
>> The information in this e-mail is intended only for the person to whom
>> it is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender
>> and properly
>> dispose of the e-mail.
>>
>>
>>
>>
>>
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Re: [Freesurfer] .label versus .thresh.label

[krista kelly]

Great thanks Bruce! I'm assuming then that using the thresh.label is the
best choice.


On Sun, Nov 17, 2013 at 12:50 PM, Bruce Fischl
wrote:

> Hi Krista
>
> the unthresholded labels give every point that has a non-zero probability
> of being in the label, no matter how unlikely. The .thresh ones are
> thresholded to pick the most likely vertices that give a label that is the
> right surface area.
>
> cheers
> Bruce
>
> On Sun, 17 Nov 2013, krista kelly wrote:
>
>  Hi, I've just started using the newest freesurfer v 5.3 and I've noticed
>> in
>> the labels folder that every .label has a thresh.label. When overlaying
>> the
>> two, they can be quite different (for example MT.label is much larger than
>> MT.thresh.label) or quite similar (V1.label is just a tiny bit larger than
>> V1.thresh.label). What is the difference between the two and which is best
>> to use?
>> Thanks!
>> Krista
>>
>>
>>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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[Freesurfer] .label versus .thresh.label

[krista kelly]

Hi, I've just started using the newest freesurfer v 5.3 and I've noticed in
the labels folder that every .label has a thresh.label. When overlaying the
two, they can be quite different (for example MT.label is much larger than
MT.thresh.label) or quite similar (V1.label is just a tiny bit larger than
V1.thresh.label). What is the difference between the two and which is best
to use?

Thanks!
Krista
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[Freesurfer] aparc.DKTatlas40

[krista kelly]

I'm using freesurfer v. 5.3 and I see a new annotation,
aparc.DKTatlas40.annot in the labels folder. Can anyone tell me what the
difference between this and the apart.annot is? Does it just have 40 labels
versus the 36 found in the older version?

Thanks!
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Re: [Freesurfer] Linux recon-all error

[krista kelly]

Thanks Alan for your response! I've tried typing sudo yum update into the
terminal window, however it does not work. It says yum:command not found.
I've tried googling how to do this, but I can't find anything. This is what
I type into the terminal window:

sudo yum command

Am I doing it wrong?

Thanks!
Krista


On Thu, Nov 14, 2013 at 10:48 AM, Alan Francis wrote:

> Hi Krista:
>
> You may want to update tcsh. You can do this by using SUDO and 'yum
> update'.
>
> best,
>
> Alan
>
>
> On Thu, Nov 14, 2013 at 10:42 AM, krista kelly 
> wrote:
>
>> Hello,
>>
>> I'm running freesurfer's recon-all using Linux and the past few subjects
>> I've run, recon-all has exited with errors. I've ran a few subjects so far
>> with no problems, and now all of a sudden there's an issue and I can't
>> figure out why. I have been able to run these "problem'  subjects using
>> Linux on other computers with no issues, so it can't be a raw data issue. I
>> have pasted the terminal window text below. If anyone has any idea why this
>> is occurring, I'd love to know!
>>
>> Thanks!
>>
>>  freesurfer-Linux-centos4-stable-pub-v5.3.0 
>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> FREESURFER_HOME   /usr/local/freesurfer
>> FSFAST_HOME   /usr/local/freesurfer/fsfast
>> FSF_OUTPUT_FORMAT nii.gz
>> SUBJECTS_DIR  /usr/local/freesurfer/subjects
>> MNI_DIR   /usr/local/freesurfer/mni
>>
>> Freesurfer Virtual Machine
>> sudo password: freesurfer
>>
>> fsuser@xubuntu-VirtualBox:~$ recon-all -all -qcache -notal-check -cw256
>> -subjid BV33 -i ~/Desktop/nii.gzs/BV33.nii.gz
>>
>> WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
>>
>> Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
>> Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
>> INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
>> Actual FREESURFER_HOME /usr/local/freesurfer
>> Linux xubuntu-VirtualBox 3.2.0-55-generic #85-Ubuntu SMP Wed Oct 2
>> 13:43:27 UTC 2013 i686 i686 i386 GNU/Linux
>> -cw256 option is now persistent (remove with -clean-cw256)
>> /usr/local/freesurfer/subjects/BV33
>>
>>  mri_convert /home/fsuser/Desktop/nii.gzs/BV33.nii.gz
>> /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz
>>
>> mri_convert /home/fsuser/Desktop/nii.gzs/BV33.nii.gz
>> /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> reading from /home/fsuser/Desktop/nii.gzs/BV33.nii.gz...
>> TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (0.999683, 0.0209404, 0.0139622)
>> j_ras = (-0.0209424, 0.999781, 0)
>> k_ras = (-0.0139591, -0.000292399, 0.03)
>> writing to /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz...
>> #
>> #@# MotionCor Thu Nov 14 10:28:28 EST 2013
>> Found 1 runs
>> /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz
>> Checking for (invalid) multi-frame inputs...
>> WARNING: only one run found. This is OK, but motion
>> correction cannot be performed on one run, so I'll
>> copy the run to rawavg and continue.
>>
>>  cp /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz
>> /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz
>>
>> /usr/local/freesurfer/subjects/BV33
>>
>>  mri_convert /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz
>> /usr/local/freesurfer/subjects/BV33/mri/orig.mgz --conform --cw256
>>
>> mri_convert /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz
>> /usr/local/freesurfer/subjects/BV33/mri/orig.mgz --conform --cw256
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> reading from /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz...
>> TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (0.999683, 0.0209404, 0.0139622)
>> j_ras = (-0.0209424, 0.999781, 0)
>> k_ras = (-0.0139591, -0.000292399, 0.03)
>> Original Data has (1, 1, 1) mm size and (176, 230, 175) voxels.
>> Data is conformed to 1 mm size and 256 voxels for all directions
>> changing data type from float to uchar (noscale = 0)...
>> MRIchangeType: Building histogram
>> Reslicing using trilinear interpolation
>> writing to /usr/local/freesurfer/subjects/BV33/mri/orig.mgz...
>>
>>  mri_add_xform_to_header -c
>> /usr/local/freesurfer/subjects/BV33/mri/transforms/talairach.xfm
>> /usr/local/freesurfer/subjects/BV33/mri/orig.mgz
>> /usr/local/freesurfe

[Freesurfer] Linux recon-all error

[krista kelly]

Hello,

I'm running freesurfer's recon-all using Linux and the past few subjects
I've run, recon-all has exited with errors. I've ran a few subjects so far
with no problems, and now all of a sudden there's an issue and I can't
figure out why. I have been able to run these "problem'  subjects using
Linux on other computers with no issues, so it can't be a raw data issue. I
have pasted the terminal window text below. If anyone has any idea why this
is occurring, I'd love to know!

Thanks!

 freesurfer-Linux-centos4-stable-pub-v5.3.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni

Freesurfer Virtual Machine
sudo password: freesurfer

fsuser@xubuntu-VirtualBox:~$ recon-all -all -qcache -notal-check -cw256
-subjid BV33 -i ~/Desktop/nii.gzs/BV33.nii.gz

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux xubuntu-VirtualBox 3.2.0-55-generic #85-Ubuntu SMP Wed Oct 2 13:43:27
UTC 2013 i686 i686 i386 GNU/Linux
-cw256 option is now persistent (remove with -clean-cw256)
/usr/local/freesurfer/subjects/BV33

 mri_convert /home/fsuser/Desktop/nii.gzs/BV33.nii.gz
/usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz

mri_convert /home/fsuser/Desktop/nii.gzs/BV33.nii.gz
/usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/fsuser/Desktop/nii.gzs/BV33.nii.gz...
TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.999683, 0.0209404, 0.0139622)
j_ras = (-0.0209424, 0.999781, 0)
k_ras = (-0.0139591, -0.000292399, 0.03)
writing to /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz...
#
#@# MotionCor Thu Nov 14 10:28:28 EST 2013
Found 1 runs
/usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.

 cp /usr/local/freesurfer/subjects/BV33/mri/orig/001.mgz
/usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz

/usr/local/freesurfer/subjects/BV33

 mri_convert /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz
/usr/local/freesurfer/subjects/BV33/mri/orig.mgz --conform --cw256

mri_convert /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz
/usr/local/freesurfer/subjects/BV33/mri/orig.mgz --conform --cw256
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /usr/local/freesurfer/subjects/BV33/mri/rawavg.mgz...
TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.999683, 0.0209404, 0.0139622)
j_ras = (-0.0209424, 0.999781, 0)
k_ras = (-0.0139591, -0.000292399, 0.03)
Original Data has (1, 1, 1) mm size and (176, 230, 175) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /usr/local/freesurfer/subjects/BV33/mri/orig.mgz...

 mri_add_xform_to_header -c
/usr/local/freesurfer/subjects/BV33/mri/transforms/talairach.xfm
/usr/local/freesurfer/subjects/BV33/mri/orig.mgz
/usr/local/freesurfer/subjects/BV33/mri/orig.mgz

INFO: extension is mgz
#
#@# Talairach Thu Nov 14 10:28:40 EST 2013
/usr/local/freesurfer/subjects/BV33/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
orig.mgz --o orig_nu.mgz

Linux xubuntu-VirtualBox 3.2.0-55-generic #85-Ubuntu SMP Wed Oct 2 13:43:27
UTC 2013 i686 i686 i386 GNU/Linux

recon-all -s BV33 exited with ERRORS at Thu Nov 14 10:29:51 EST 2013

For more details, see the log file
/usr/local/freesurfer/subjects/BV33/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

fsuser@xubuntu-VirtualBox:~$ open
/usr/local/freesurfer/subjects/BV33/scripts/recon-all
Couldn't get a file descriptor referring to the console
fsuser@xubuntu-VirtualBox:~$
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[Freesurfer] Mac issue

[krista kelly]

To all my fellow Freesurfers...

Has anyone had any issues with doing recon-all on a Mac. I'm having a
problem with the automatically generated labels V1, V2, and MT (when loaded
in tksurfer there are holes in the mask) and I've been informed that this
may be an issue because of running the program on a mac instead of using
linux.

I'm concerned that if the labels are incorrect, that there may also be a
problem with the atlases and doing any whole brain analyses (although the
atlas masks and surfs look fine). If anyone else has encountered this issue
and can shed light on it for me, I would appreciate it!

Best,
Krista
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Re: [Freesurfer] V1 Labels (fwd)

[krista kelly]

Hi again,

I apologize for all of the emails, but I'm really trying to figure out what
this labelling problem is. I've gone through all of my participants and for
most of them, the talairach is fine and the voxel size is 1 x 1 x 1mm, so
having a high resolution cannot be the problem, unless the problem is with
the fact that it was a 3T scanner and not 1.5T. Could this be it?

Can I upload a participant who's talairaching is fine and voxel size is 1 x
1 x 1mm so that you might be able to figure out what the problem with
mapping the labels is? Also, I'd like to do a whole brain analyses prior to
a ROI analysis with the atlases and labels, but I want to make sure that I
can trust the data that I have without having to rerun all of my
participants.

Thanks!
Krista


On Wed, Oct 9, 2013 at 9:15 PM, krista kelly wrote:

> Hi again Allison,
>
> After going through a few of my subjects' data, I've realized that only
> that one person has problems with the talairach.xfm, all of the others look
> fine yet the problem with the labels still persists. Could it still be the
> high resolution problem that's causing the label problem? I can upload a
> participant's data that does not have a bad tal transform if that helps.
> Just let me know.
>
> Thanks!
> Krista
>
>
> On Wed, Oct 9, 2013 at 9:04 PM, krista kelly wrote:
>
>> Sorry, just one last thing. If the pial matter and white matter borders
>> came out fine initially, is it necessary to rerun the whole recon-all
>> automatic pipeline? I'm just asking because I have about 40 people that i
>> will need to rerun because of this problem.
>>
>> Thanks again!
>> Krista
>>
>>
>> On Wed, Oct 9, 2013 at 8:47 PM, krista kelly wrote:
>>
>>> Also, just to add to this, if I rerun recon in 5.1 starting from the
>>> normalization stage when I initially ran all subjects in 5.0, will this be
>>> a problem?
>>>
>>>
>>>
>>>
>>> On Wed, Oct 9, 2013 at 8:05 PM, krista kelly 
>>> wrote:
>>>
>>>> Thanks Allison,
>>>>
>>>> So to be clear, I just need to rename talairach.auto.xfm as
>>>> talairach.xfm and then rerun recon-all from the normalization step? 
>>>> However,
>>>> I'm not sure how to run recon starting from the normalization stage. Would
>>>> you be able to help with that?
>>>>
>>>> Also, I've been doing manual edits to the brain extraction as well as
>>>> adding control points on all of my subjects and I'm wondering if this will
>>>> negate any edits I've made. So I'm pretty much starting from scratch?
>>>>
>>>> Thanks so much for looking into this for me!
>>>>
>>>> Best,
>>>> Krista
>>>>
>>>>
>>>> On Mon, Oct 7, 2013 at 12:19 PM, Allison Stevens <
>>>> astev...@nmr.mgh.harvard.edu> wrote:
>>>>
>>>>> Hi Krista,
>>>>> I took a look at your subject and think I have determined the problem.
>>>>> Because your input data was high resolution (1. x 0.9375 x 0.9375), 
>>>>> the
>>>>> talairach registration step failed. If you look at the talairach.xfm,
>>>>> you'll see it is way off:
>>>>> tkregister2 --mgz --s BV20_2ndrun --fstal --surf orig
>>>>>
>>>>> But the talairach.auto.xfm is correct. You can copy the
>>>>> talairach.auto.xfm to talairach.xfm and rerun from the -normalization 
>>>>> step.
>>>>>
>>>>> You might also want to look at these instructions:
>>>>> https://surfer.nmr.mgh.**harvard.edu/fswiki/HiResRecon<https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon>
>>>>>
>>>>> They might not all apply to you but could potentially.
>>>>> Allison
>>>>>
>>>>>
>>>>>
>>>>>  -- Forwarded message --
>>>>>> Date: Thu, 03 Oct 13 22:55:12 -0400
>>>>>> From: krista.kell...@gmail.com
>>>>>> To: fis...@nmr.mgh.harvard.edu
>>>>>> Subject: V1 Labels
>>>>>>
>>>>>> Hey!
>>>>>>
>>>>>> Krista  (krista.kell...@gmail.com) has uploaded some files for you
>>>>>> at the Martinos Center FileDrop:
>>>>>>
>>>>>> -> BV20_2ndrun.zip (167.53 MiB) <http://gate.nmr.mgh.harvard.**
>>>>>> edu/filedrop2/?u=1079qbdf&f=**dzep9n4<http:/

Re: [Freesurfer] V1 Labels (fwd)

[krista kelly]

Sorry, just one last thing. If the pial matter and white matter borders
came out fine initially, is it necessary to rerun the whole recon-all
automatic pipeline? I'm just asking because I have about 40 people that i
will need to rerun because of this problem.

Thanks again!
Krista


On Wed, Oct 9, 2013 at 8:47 PM, krista kelly wrote:

> Also, just to add to this, if I rerun recon in 5.1 starting from the
> normalization stage when I initially ran all subjects in 5.0, will this be
> a problem?
>
>
>
>
> On Wed, Oct 9, 2013 at 8:05 PM, krista kelly wrote:
>
>> Thanks Allison,
>>
>> So to be clear, I just need to rename talairach.auto.xfm as talairach.xfm and
>> then rerun recon-all from the normalization step? However, I'm not sure
>> how to run recon starting from the normalization stage. Would you be able
>> to help with that?
>>
>> Also, I've been doing manual edits to the brain extraction as well as
>> adding control points on all of my subjects and I'm wondering if this will
>> negate any edits I've made. So I'm pretty much starting from scratch?
>>
>> Thanks so much for looking into this for me!
>>
>> Best,
>> Krista
>>
>>
>> On Mon, Oct 7, 2013 at 12:19 PM, Allison Stevens <
>> astev...@nmr.mgh.harvard.edu> wrote:
>>
>>> Hi Krista,
>>> I took a look at your subject and think I have determined the problem.
>>> Because your input data was high resolution (1. x 0.9375 x 0.9375), the
>>> talairach registration step failed. If you look at the talairach.xfm,
>>> you'll see it is way off:
>>> tkregister2 --mgz --s BV20_2ndrun --fstal --surf orig
>>>
>>> But the talairach.auto.xfm is correct. You can copy the
>>> talairach.auto.xfm to talairach.xfm and rerun from the -normalization step.
>>>
>>> You might also want to look at these instructions:
>>> https://surfer.nmr.mgh.**harvard.edu/fswiki/HiResRecon<https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon>
>>>
>>> They might not all apply to you but could potentially.
>>> Allison
>>>
>>>
>>>
>>>  -- Forwarded message --
>>>> Date: Thu, 03 Oct 13 22:55:12 -0400
>>>> From: krista.kell...@gmail.com
>>>> To: fis...@nmr.mgh.harvard.edu
>>>> Subject: V1 Labels
>>>>
>>>> Hey!
>>>>
>>>> Krista  (krista.kell...@gmail.com) has uploaded some files for you at
>>>> the Martinos Center FileDrop:
>>>>
>>>> -> BV20_2ndrun.zip (167.53 MiB) <http://gate.nmr.mgh.harvard.**
>>>> edu/filedrop2/?u=1079qbdf&f=**dzep9n4<http://gate.nmr.mgh.harvard.edu/filedrop2/?u=1079qbdf&f=dzep9n4>
>>>> >
>>>>
>>>> Also, they left this message for you:
>>>> Hi Bruce,
>>>>
>>>> Here is a zipped file of one of the subjects that I'm having label
>>>> troubles with. The lh.v1.label isn't mapping correctly. I find the same
>>>> goes for the aparc atlas as well (I haven't checked out anything else). If
>>>> you could help me figure out why this is happening, that would be great!
>>>>
>>>> Thanks,
>>>> Krista
>>>>
>>>> Please be aware, your upload will expire on December 31st. If you'd
>>>> like to download these files, feel free to use the link below:
>>>>
>>>> http://gate.nmr.mgh.harvard.**edu/filedrop2/?u=1079qbdf<http://gate.nmr.mgh.harvard.edu/filedrop2/?u=1079qbdf>
>>>>
>>>> Cheers,
>>>> The NMR Team
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>.
>>>  If the e-mail was sent to you in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>
>
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Re: [Freesurfer] V1 Labels (fwd)

[krista kelly]

Also, just to add to this, if I rerun recon in 5.1 starting from the
normalization stage when I initially ran all subjects in 5.0, will this be
a problem?




On Wed, Oct 9, 2013 at 8:05 PM, krista kelly wrote:

> Thanks Allison,
>
> So to be clear, I just need to rename talairach.auto.xfm as talairach.xfm and
> then rerun recon-all from the normalization step? However, I'm not sure
> how to run recon starting from the normalization stage. Would you be able
> to help with that?
>
> Also, I've been doing manual edits to the brain extraction as well as
> adding control points on all of my subjects and I'm wondering if this will
> negate any edits I've made. So I'm pretty much starting from scratch?
>
> Thanks so much for looking into this for me!
>
> Best,
> Krista
>
>
> On Mon, Oct 7, 2013 at 12:19 PM, Allison Stevens <
> astev...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Krista,
>> I took a look at your subject and think I have determined the problem.
>> Because your input data was high resolution (1. x 0.9375 x 0.9375), the
>> talairach registration step failed. If you look at the talairach.xfm,
>> you'll see it is way off:
>> tkregister2 --mgz --s BV20_2ndrun --fstal --surf orig
>>
>> But the talairach.auto.xfm is correct. You can copy the
>> talairach.auto.xfm to talairach.xfm and rerun from the -normalization step.
>>
>> You might also want to look at these instructions:
>> https://surfer.nmr.mgh.**harvard.edu/fswiki/HiResRecon<https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon>
>>
>> They might not all apply to you but could potentially.
>> Allison
>>
>>
>>
>>  -- Forwarded message --
>>> Date: Thu, 03 Oct 13 22:55:12 -0400
>>> From: krista.kell...@gmail.com
>>> To: fis...@nmr.mgh.harvard.edu
>>> Subject: V1 Labels
>>>
>>> Hey!
>>>
>>> Krista  (krista.kell...@gmail.com) has uploaded some files for you at
>>> the Martinos Center FileDrop:
>>>
>>> -> BV20_2ndrun.zip (167.53 MiB) <http://gate.nmr.mgh.harvard.**
>>> edu/filedrop2/?u=1079qbdf&f=**dzep9n4<http://gate.nmr.mgh.harvard.edu/filedrop2/?u=1079qbdf&f=dzep9n4>
>>> >
>>>
>>> Also, they left this message for you:
>>> Hi Bruce,
>>>
>>> Here is a zipped file of one of the subjects that I'm having label
>>> troubles with. The lh.v1.label isn't mapping correctly. I find the same
>>> goes for the aparc atlas as well (I haven't checked out anything else). If
>>> you could help me figure out why this is happening, that would be great!
>>>
>>> Thanks,
>>> Krista
>>>
>>> Please be aware, your upload will expire on December 31st. If you'd like
>>> to download these files, feel free to use the link below:
>>>
>>> http://gate.nmr.mgh.harvard.**edu/filedrop2/?u=1079qbdf<http://gate.nmr.mgh.harvard.edu/filedrop2/?u=1079qbdf>
>>>
>>> Cheers,
>>> The NMR Team
>>>
>>>
>>>
>>>
>>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>.
>>  If the e-mail was sent to you in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
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Re: [Freesurfer] V1 Labels (fwd)

[krista kelly]

Thanks Allison,

So to be clear, I just need to rename talairach.auto.xfm as talairach.xfm and
then rerun recon-all from the normalization step? However, I'm not sure how
to run recon starting from the normalization stage. Would you be able to
help with that?

Also, I've been doing manual edits to the brain extraction as well as
adding control points on all of my subjects and I'm wondering if this will
negate any edits I've made. So I'm pretty much starting from scratch?

Thanks so much for looking into this for me!

Best,
Krista


On Mon, Oct 7, 2013 at 12:19 PM, Allison Stevens <
astev...@nmr.mgh.harvard.edu> wrote:

> Hi Krista,
> I took a look at your subject and think I have determined the problem.
> Because your input data was high resolution (1. x 0.9375 x 0.9375), the
> talairach registration step failed. If you look at the talairach.xfm,
> you'll see it is way off:
> tkregister2 --mgz --s BV20_2ndrun --fstal --surf orig
>
> But the talairach.auto.xfm is correct. You can copy the talairach.auto.xfm
> to talairach.xfm and rerun from the -normalization step.
>
> You might also want to look at these instructions:
> https://surfer.nmr.mgh.**harvard.edu/fswiki/HiResRecon
>
> They might not all apply to you but could potentially.
> Allison
>
>
>
>  -- Forwarded message --
>> Date: Thu, 03 Oct 13 22:55:12 -0400
>> From: krista.kell...@gmail.com
>> To: fis...@nmr.mgh.harvard.edu
>> Subject: V1 Labels
>>
>> Hey!
>>
>> Krista  (krista.kell...@gmail.com) has uploaded some files for you at
>> the Martinos Center FileDrop:
>>
>> -> BV20_2ndrun.zip (167.53 MiB) > edu/filedrop2/?u=1079qbdf&f=**dzep9n4
>> >
>>
>> Also, they left this message for you:
>> Hi Bruce,
>>
>> Here is a zipped file of one of the subjects that I'm having label
>> troubles with. The lh.v1.label isn't mapping correctly. I find the same
>> goes for the aparc atlas as well (I haven't checked out anything else). If
>> you could help me figure out why this is happening, that would be great!
>>
>> Thanks,
>> Krista
>>
>> Please be aware, your upload will expire on December 31st. If you'd like
>> to download these files, feel free to use the link below:
>>
>> http://gate.nmr.mgh.harvard.**edu/filedrop2/?u=1079qbdf
>>
>> Cheers,
>> The NMR Team
>>
>>
>>
>>
>>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/**complianceline.
>  If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] Fwd: Fwd: V1 label

[krista kelly]

Sure! Where/how do I upload the subject's folder? I've tried attaching a
zipped copy to my email but it exceeds the size limit.

Thanks!
Krista


On Thu, Oct 3, 2013 at 8:23 AM, Bruce Fischl wrote:

> Hi Krista
>
> I've never seen that happen before. Can you upload this subject and we
> will take a look?
>
> thanks
> Bruce
>
> On Wed, 2 Oct 2013, krista kelly wrote:
>
>
>> Hi Bruce,
>> I've tried twice to post this to the freesurfer mail list but it hasn't
>> worked, I'm assuming because of the attached pictures. I'm going to try
>> this
>> again with only one picture and see if it works.
>>
>> I'm using the V1 labels that are automatically generated during recon-all
>> (I
>> think at autorecon step 28??). There are also V2 and MT labels that get
>> generated. Are they the Hinds ones? I'm using freesurfer version 5.0 and
>> have tried in 5.1 as well.
>>
>> Here are the commands I ran:
>>
>> recon-all -all -notal-check -cw256 -force -subjid BV20 -i
>> ~/Desktop/New_CT_niis/BV20.**nii.gz
>>
>> By holes, I mean that when I look at the label on the 3d brain in
>> tksurfer,
>> there are areas on the surface that are coloured in by the label. I've
>> attached a photograph of the left hemisphere with the V1 label overlaid.
>> It's even worse, and in both hemispheres, when I look at the cuneus label
>> automatically generated with freesurfer. Is there something I'm doing
>> wrong?
>>  Please let me know you're not able to see the snapshots.
>>
>> Thanks!
>> Krista
>>
>>
>> On Mon, Sep 23, 2013 at 5:10 PM, Bruce Fischl > >
>> wrote:
>>   Hi Krista,
>>
>>   which V1 label are you talking about? And when you say holes
>>   when you load it onto the 3D brain with tksurfer, what exactly
>>   do you mean? Can you send us a snapshot?
>>   Bruce
>>
>>
>>   On Mon, 23 Sep 2013, krista kelly wrote:
>>
>> Hi all,
>> I'm having trouble with V1 labels that are mapped
>> automatically in freesurfer. I've noticed that there
>> are holes in the label when I load it onto a 3d
>> brain in tksurfer. This happens more often for the
>> left
>> hemisphere and not so much for the right. I've found
>> the problem persists even after doing manual edits
>> of the borders and fixing the brain extraction. I
>> was just wondering if anyone has had the same
>> problem
>> or knows how to fix it (see message previously
>> posted below).
>>
>> Thanks!
>>
>> Hi Doug,
>>
>> Sorry it's been a while since I've ran the initial
>> codes, but I think these are the labels
>> automatically
>> generated by Freesurfer v5.0 during recon-all
>> (correct me if I'm wrong). Here's what I ran below:
>>
>> recon-all -all -notal-check -cw256 -force -subjid
>> MB18 -i ~/Desktop/New_CT_niis/MB18.**nii.gz
>>
>> then
>>
>> recon-all -force -s MB18 -qcache -i
>> ~/Desktop/New_CT_niis/MB18.**nii.gz
>>
>> I've checked a few more brains and noticed the same
>> problem. I've also noticed that the left hemisphere
>> is always worse than the right.  When opening the
>> brains in tkmedit, the labels are not continuous on
>> the
>> surface. Could this be the problem?  Is this label
>> the same as the Hinds label and if not, should I run
>> that instead?
>>
>>     Is possible to edit the label, and if so, how often
>> does one have to edit the labels automatically
>> created by freesurfer? I know that too much editing
>> can take away from the standardization of the
>> process
>> and I wouldn't want to mess with that too much.
>>
>>
>> Thanks!
>>
>>
>>
>> On Tue, Sep 10, 2013 at 6:35 PM, Douglas N Greve
>>  wrote:
>> >
>> > How did you do the transfer? What was your cmd
>> line?
>> > doug
>> >
>> > On 09/10/2013 05:31 

[Freesurfer] Fwd: V1 label

[krista kelly]

Hi all,

I'm having trouble with V1 labels that are mapped automatically in
freesurfer. I've noticed that there are holes in the label when I load it
onto a 3d brain in tksurfer. This happens more often for the left
hemisphere and not so much for the right. I've found the problem persists
even after doing manual edits of the borders and fixing the brain
extraction. I was just wondering if anyone has had the same problem or
knows how to fix it (see message previously posted below).

Thanks!

Hi Doug,

Sorry it's been a while since I've ran the initial codes, but I think these
are the labels automatically generated by Freesurfer v5.0 during recon-all
(correct me if I'm wrong). Here's what I ran below:

recon-all -all -notal-check -cw256 -force -subjid MB18 -i
~/Desktop/New_CT_niis/MB18.nii.gz

then

recon-all -force -s MB18 -qcache -i ~/Desktop/New_CT_niis/MB18.nii.gz

I've checked a few more brains and noticed the same problem. I've also
noticed that the left hemisphere is always worse than the right.  When
opening the brains in tkmedit, the labels are not continuous on the
surface. Could this be the problem?  Is this label the same as the Hinds
label and if not, should I run that instead?

Is possible to edit the label, and if so, how often does one have to edit
the labels automatically created by freesurfer? I know that too much
editing can take away from the standardization of the process and I
wouldn't want to mess with that too much.


Thanks!



On Tue, Sep 10, 2013 at 6:35 PM, Douglas N Greve 
wrote:
>
> How did you do the transfer? What was your cmd line?
> doug
>
> On 09/10/2013 05:31 PM, krista kelly wrote:
> > Hello,
> >
> > I am looking at cortical thickness and surface area using Freesurfer.
> > I have transferred label V1 from freesurfer onto the brains of my
> > participants and when I view them on the inflated brains in tksurfer ,
> > I notice that there are holes in the label. Is this an issue when
> > calculating mean cortical thickness and total surface area
> > estimations? Should I fill these in somehow?
> >
> > I've attached a picture to show as an example. Please let me know if
> > the picture cannot be viewed.
> >
> > Thanks!
> > Krista
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
is
> addressed. If you believe this e-mail was sent to you in error and the
e-mail
> contains patient information, please contact the Partners Compliance
HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
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> but does not contain patient information, please contact the sender and
properly
> dispose of the e-mail.
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Re: [Freesurfer] V1 label

[krista kelly]

Hi Doug,

Sorry it's been a while since I've ran the initial codes, but I think these
are the labels automatically generated by Freesurfer v5.0 during recon-all
(correct me if I'm wrong). Here's what I ran below:

recon-all -all -notal-check -cw256 -force -subjid MB18 -i
~/Desktop/New_CT_niis/MB18.nii.gz

then

recon-all -force -s MB18 -qcache -i ~/Desktop/New_CT_niis/MB18.nii.gz

I've checked a few more brains and noticed the same problem. I've also
noticed that the left hemisphere is always worse than the right.  When
opening the brains in tkmedit, the labels are not continuous on the
surface. Could this be the problem?  Is this label the same as the Hinds
label and if not, should I run that instead?

Is possible to edit the label, and if so, how often does one have to edit
the labels automatically created by freesurfer? I know that too much
editing can take away from the standardization of the process and I
wouldn't want to mess with that too much.


Thanks!



On Tue, Sep 10, 2013 at 6:35 PM, Douglas N Greve 
wrote:
>
> How did you do the transfer? What was your cmd line?
> doug
>
> On 09/10/2013 05:31 PM, krista kelly wrote:
> > Hello,
> >
> > I am looking at cortical thickness and surface area using Freesurfer.
> > I have transferred label V1 from freesurfer onto the brains of my
> > participants and when I view them on the inflated brains in tksurfer ,
> > I notice that there are holes in the label. Is this an issue when
> > calculating mean cortical thickness and total surface area
> > estimations? Should I fill these in somehow?
> >
> > I've attached a picture to show as an example. Please let me know if
> > the picture cannot be viewed.
> >
> > Thanks!
> > Krista
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
is
> addressed. If you believe this e-mail was sent to you in error and the
e-mail
> contains patient information, please contact the Partners Compliance
HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
error
> but does not contain patient information, please contact the sender and
properly
> dispose of the e-mail.
>
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[Freesurfer] Fwd: Segmentation edits

[krista kelly]

Just wanted to resend these questions to see if anyone has any answers.
Thanks!

I am doing cortical thickness and surface area analyses and had a few
questions regarding editing the borders.

1) Is it reasonable to edit every (big and small) error that I find?
Basically, how much a difference would it make in terms of the surface area
and cortical thickness values if I did not edit the smaller errors?

2) If the skull hasn't been completely stripped, but is not designated as
either white or gray matter, do I need to adjust the thresholding for
extracting the brain and re-extract? The only situation in which I feel
this would be a problem is when doing whole brain analyses.

3) Would it make a difference to the data if I initially ran recon-all
using freesurfer version 5.0 and then, after editing the
segmentations/labels/skullstripping, reran autorecon 2,or 3 using
freesurfer version 5.1?

If anyone could answer any or all of these questions that would be great!
Krista
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[Freesurfer] Segmentation edits

[krista kelly]

Hi all,

I am doing cortical thickness and surface area analyses and had a few
questions regarding editing the borders.

1) Is it reasonable to edit every (big and small) error that I find?
Basically, how much a difference would it make in terms of the surface area
and cortical thickness values if I did not edit the smaller errors?

2) If the skull hasn't been completely stripped, but is not designated as
either white or gray matter, do I need to adjust the thresholding for
extracting the brain and re-extract? The only situation in which I feel
this would be a problem is when doing whole brain analyses.

3) Would it make a difference to the data if I initially ran recon-all
using freesurfer version 5.0 and then, after editing the
segmentations/labels/skullstripping, reran autorecon 2,or 3 using
freesurfer version 5.1?

If anyone could answer any or all of these questions that would be great!
Krista
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[Freesurfer] Freesurfer version for processed data

[krista kelly]

Hello,

Is there any way to find out which Freesurfer version I used to process
data?

Thanks,
Krista
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[Freesurfer] Download v. 5.0 on Mac Lion 10.7.5

[krista kelly]

Hello,

I need to download an older version of freesurfer (Version 5.0) on a Mac
Lion 10.7.5. In the archives I don't see a file for Lion, just Leopard and
Tiger. Is it possible that either of these will work for Lion? Also, are
there any step by step instructions on how to install?

Thanks!
Krista
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[Freesurfer] mris_anatomical stats different thickness files

[krista kelly]

I'm looking at both cortical thickness and surface area differences between
two groups. I've been using mris_anatomical_stats to retrieve values but had
a few questions:

1) Do I need to do separate mris_anatomical_stats using different thickness
files (bolded below) to get cortical thickness and surface area measures.
For example:

cortical thickness - mris_anatomical_stats -l lh.v1.label -t
*lh.thickness*-b -f BV01/stats/lh.v1.stats BV01 lh
surface area - mris_anatomical_stats -l lh.v1.label -t *lh.area *-b -f
BV01/stats/lh.v1.stats BV01 lh

 Or, since the output files include all of these measures, is it fine to
just run one of the two?

2) The output files for both analyses run above (with different thickness
files) have identical values for everything except for tray matter volume.
Using lh.thickness file - grayvol = 8082; using lh.area file - grayvol =
4029. Can anyone clarify why this happens?

3) The default surface area values are for the white matter surface. How do
I run mri_anatomical_stats to get the pial surface? I've
tried mris_anatomical_stats -l lh.v1.label -t *lh.area.pial *-b -f
BV01/stats/lh.v1.stats BV01 lh but I get identical values for everything
(except grayvol).

Thanks!
Krista
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[Freesurfer] Surface area measure

[krista kelly]

When  I extract surface area data using the following commands, which
measure of surface area am I getting, the pial surface, the WM surface, or
the total of both combined?

aparcstats2table --subjects 1 2 3 4 --parc aparc.a2009 --hemi rh --meas area
--tablefile aparc_stats_rh.txt

Thanks!
Krista
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[Freesurfer] QDec questions

[krista kelly]

Hi, just wondering if anyone has any advice on the following questions:

I'm using QDEC to analyze cortical thickness differences between groups and
I have a few questions:

1) There are a few variables that I need to control for. First variable is
scanner - I used two different scanners of different field strengths (1.5T
GE and 3T Siemens) so I wanted to control for scanner. I also wanted to
control for age and gender. Here's my ideal design setup:

discrete variables - groups, scanner, gender
nuisance variable - age

contrast would be 1 -1 0 0 0 0

I realize that scanner, gender, and group are all discrete variables, and
that age would be a continuous one. However, in the design tab, I am not
able to select all 3 discrete variables (groups, scanner, and gender).
Should I designate scanner or gender as a nuisance variable instead? Would
it matter which one I use as the nuisance variable? Possible setup:

discrete vars - groups, scanner
nuisance vars - age, gender

contrast - 1 -1 0 0 (Correct?)

2) If I use DODS, should I demean the ages if age is a nuisance variable?

3) If I use a smoothing kernel during the analysis, then create an ROI and
map that ROI to each individual subject, will the resulting .stats file in
each subjects stats folder reflect the smoothed data or does mapping onto
each ROI just extract the raw unsmoothed data from each vertex?

Thanks!
Krista
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[Freesurfer] QDEC labels vs annotations

[krista kelly]

I'm using the labels saved in QDEC to extract cortical thickness values for
certain regions. For example, I've used the lh.v1.label to map onto the
fsaverage brain and then to map this onto each individual subject. When I
load the lh.PALS_B12_Brodmann.annot or the lh.PALS_B12_Visuotopic.annot onto
the fasaverage brain, the areas that are named v1 do not quite match up with
the actual lh.v1.label. The more inferior part of the lh.v1.label is
considered v2 in the the annotation space. Should I be worried about this?
Or can I still use the lh.v1.label to extract information for v1 (even
though the annotation file would consider it v2).

Thanks!
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[Freesurfer] QDEC analysis

[krista kelly]

I'm using QDEC to analyze cortical thickness differences between groups and
I have a few questions:

1) There are a few variables that I need to control for. First variable is
scanner - I used two different scanners of different field strengths (1.5T
GE and 3T Siemens) so I wanted to control for scanner. I also wanted to
control for age and gender. Here's my ideal design setup:

discrete variables - groups, scanner, gender
nuisance variable - age

contrast would be 1 -1 0 0 0 0

I realize that scanner, gender, and group are all discrete variables, and
that age would be a continuous one. However, in the design tab, I am not
able to select all 3 discrete variables (groups, scanner, and gender).
Should I designate scanner or gender as a nuisance variable instead? Would
it matter which one I use as the nuisance variable? Possible setup:

discrete vars - groups, scanner
nuisance vars - age, gender

contrast - 1 -1 0 0 (Correct?)

2) If I use DODS, should I demean the ages if age is a nuisance variable?

3) If I use a smoothing kernel during the analysis, then create an ROI and
map that ROI to each individual subject, will the resulting .stats file in
each subjects stats folder reflect the smoothed data or does mapping onto
each ROI just extract the raw unsmoothed data from each vertex?

Thanks!
Krista
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[Freesurfer] stop receiving emails

[Krista Kelly]

How do I stop receiving emails from everyone asking and responding to
questions about FreeSurfer?
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[Freesurfer] Compiling stats file for ROI label in QDec

[Krista Kelly]

Using QDec, I've created an ROI label (lh.G_cuneus.label) and a .stats
file (lh.G_cuneus.stats) that corresponds to this ROI for each participant
in my group. Is there a quick way to compile cortical thickness data for
this ROI from all participants? The manual suggests using aparcstats2table
but I'm not sure how to select the stats for just this one ROI. Any help
would be appreciated!
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dispose of the e-mail.

[Freesurfer] Compiling stats file for ROI label in QDec

[Krista Kelly]

Using QDec, I've created an ROI label (lh.G_cuneus.label) and a .stats
file (lh.G_cuneus.stats) that corresponds to this ROI for each participant
in my group. Is there a quick way to compile cortical thickness data for
this ROI from all participants? The manual suggests using aparcstats2table
but I'm not sure how to select the stats for just this one ROI. Any help
would be appreciated!
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[Freesurfer] Comparison between two hemispheres using QDEC.

[Krista Kelly]

I'm using QDEC to analyze cortical thickness of a patient population
compared to controls. One of the things I wanted to analyze is the
difference between hemispheres within patients. It seems that I can only
analyze one hemisphere at a time in QDEC; is there any way to analyze the
difference BETWEEN hemispheres for one group?

Thank you!
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