subject:"\[Freesurfer\] LGI"

External Email - Use Caution

Perfect that has worked.

Thank you so much for your help!

Have a great weekend,
Luke

> On 2 Dec 2022, at 16:57, Luke K Harper  wrote:
> 
> Thanks! 
> 
> As the subject ID in my example is A152 should this be replaced by $subj in 
> the label section too?  Each individual has a label created via label2label 
> from a label on fsaverage or does this not matter?
> 
> Best,
> Luke
> 
>> On 2 Dec 2022, at 16:46, Huang, Yujing > <mailto:yhuan...@mgh.harvard.edu>> wrote:
>> 
>> Sorry, ‘Done’ should be in all lower case.
>>  
>> for subj in `ls -1`
>> do
>> echo "mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label 
>> --i $SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum 
>> $SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats"
>> #mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label --i 
>> $SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum 
>> $SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats
>> done
>>  
>> 1. remove the commented out line # first to verify echo printout
>> 2. add back the line w/o the # sign
>>  
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>> > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Huang, Yujing
>> Sent: Friday, December 2, 2022 10:34 AM
>> To: Freesurfer support list > <mailto:freesurfer@nmr.mgh.harvard.edu>>
>> Subject: Re: [Freesurfer] LGI label statistics
>>  
>> Hi Luke,
>>  
>> I don’t know any bash script available to perform the batch job.
>>  
>> You can enter it in a for loop at prompt. From your $SUBJECTS_DIR,
>>  
>> for subj in `ls -1`
>> do
>> echo "mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label 
>> --i $SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum 
>> $SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats"
>> #mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label --i 
>> $SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum 
>> $SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats
>> Done
>>  
>> I commented out the command submitting mri_segstat. I always verify the 
>> printout from the echo first before submitting the jobs.
>>  
>> Hope this helps.
>>  
>> Best,
>>  
>> Yujing
>>  
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>> > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Luke K Harper
>> Sent: Friday, December 2, 2022 10:08 AM
>> To: Freesurfer support list > <mailto:freesurfer@nmr.mgh.harvard.edu>>
>> Subject: Re: [Freesurfer] LGI label statistics
>>  
>> External Email - Use Caution
>> 
>> Hi Yujing
>>  
>> Ah great, Thank you so much for your help! That was the answer. I have been 
>> able to extract the stats now using the following script:
>>  
>> mri_segstats --slabel A152 rh $SUBJECTS_DIR/A152/label/rh.c1.label --i 
>> $SUBJECTS_DIR/A152/surf/rh.pial_lgi --sum 
>> $SUBJECTS_DIR/A152/stats/rh.c1.pial_lgi.stats
>>  
>> I have 186 individuals and have been trying to extract each individuals 
>> statistics individually, do you know if there is a bash shell script 
>> available to perform this process on all individuals in my study at once?
>>  
>> Best,
>> Luke
>>  
>>  
>> 
>> On 2 Dec 2022, at 15:28, Huang, Yujing > <mailto:yhuan...@mgh.harvard.edu>> wrote:
>>  
>> Hi Luke,
>>  
>> Can you try to pass the full path to your label file?  Instead of 
>> ‘rh.c1.label’, pass 
>> ‘/Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label’ to mri_segstats.
>>  
>> I think that should work.
>>  
>> Best,
>>  
>> Yujing
>>  
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>> > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Luke K Harper
>> Sent: Friday, December 2, 2022 5:14 AM
>> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
>> Subject: [Freesurfer] LGI label statistics
>>  
>> External Email - Use Caution
>> Dear freesurfer,
>>  
>> I am attempting to extract LGI statistical data from a label running the 
>> mri_segstats command
>>  
>> Here is the script I am attempting to run:
>>  
>> mri_segstats --slabel A152 rh rh.c1.label --i 
>>

Re: [Freesurfer] LGI label statistics

Yes, replace A152 in your example with $subj. I’m assuming there are 
label/rh.c1.label and surf/rh.pial_lgi in each individual subjects.

Not sure I understand your second question.

Best,

Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Luke K Harper
Sent: Friday, December 2, 2022 10:57 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] LGI label statistics


External Email - Use Caution
Thanks!

As the subject ID in my example is A152 should this be replaced by $subj in the 
label section too?  Each individual has a label created via label2label from a 
label on fsaverage or does this not matter?

Best,
Luke


On 2 Dec 2022, at 16:46, Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:

Sorry, ‘Done’ should be in all lower case.

for subj in `ls -1`
do
echo "mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label --i 
$SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum 
$SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats"
#mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label --i 
$SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum 
$SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats
done

1. remove the commented out line # first to verify echo printout
2. add back the line w/o the # sign

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Huang, Yujing
Sent: Friday, December 2, 2022 10:34 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] LGI label statistics

Hi Luke,

I don’t know any bash script available to perform the batch job.

You can enter it in a for loop at prompt. From your $SUBJECTS_DIR,

for subj in `ls -1`
do
echo "mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label --i 
$SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum 
$SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats"
#mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label --i 
$SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum 
$SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats
Done

I commented out the command submitting mri_segstat. I always verify the 
printout from the echo first before submitting the jobs.

Hope this helps.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Luke K Harper
Sent: Friday, December 2, 2022 10:08 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] LGI label statistics

External Email - Use Caution
Hi Yujing

Ah great, Thank you so much for your help! That was the answer. I have been 
able to extract the stats now using the following script:

mri_segstats --slabel A152 rh $SUBJECTS_DIR/A152/label/rh.c1.label --i 
$SUBJECTS_DIR/A152/surf/rh.pial_lgi --sum 
$SUBJECTS_DIR/A152/stats/rh.c1.pial_lgi.stats

I have 186 individuals and have been trying to extract each individuals 
statistics individually, do you know if there is a bash shell script available 
to perform this process on all individuals in my study at once?

Best,
Luke


On 2 Dec 2022, at 15:28, Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:

Hi Luke,

Can you try to pass the full path to your label file?  Instead of 
‘rh.c1.label’, pass ‘/Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label’ 
to mri_segstats.

I think that should work.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Luke K Harper
Sent: Friday, December 2, 2022 5:14 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] LGI label statistics

External Email - Use Caution
Dear freesurfer,

I am attempting to extract LGI statistical data from a label running the 
mri_segstats command

Here is the script I am attempting to run:

mri_segstats --slabel A152 rh rh.c1.label --i 
$SUBJECTS_DIR/A152/surf/rh.pial_lgi --sum rh.aparc.pial_lgi.stats

This returns an error: error: mri_segstats: could not open label file 
rh.c1.label

I created the label using freeview - make closed path - then filling the closed 
path. The label projects on pial and inflated surfaces
Furthermore the label is able to be identified and used in the following command

mris_anatomical_stats \
-l /Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label \
-f /Users/lu8342ha/Desktop/subjects/A152/stats/rh.c1.stats \
A152 \
rh

Please could you advise me on where I am going wrong here?

Many thanks,

Luke
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claiming to

Re: [Freesurfer] LGI label statistics

External Email - Use Caution

Thanks! 

As the subject ID in my example is A152 should this be replaced by $subj in the 
label section too?  Each individual has a label created via label2label from a 
label on fsaverage or does this not matter?

Best,
Luke

> On 2 Dec 2022, at 16:46, Huang, Yujing  wrote:
> 
> Sorry, ‘Done’ should be in all lower case.
>  
> for subj in `ls -1`
> do
> echo "mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label --i 
> $SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum 
> $SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats"
> #mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label --i 
> $SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum 
> $SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats
> done
>  
> 1. remove the commented out line # first to verify echo printout
> 2. add back the line w/o the # sign
>  
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of Huang, Yujing
> Sent: Friday, December 2, 2022 10:34 AM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] LGI label statistics
>  
> Hi Luke,
>  
> I don’t know any bash script available to perform the batch job.
>  
> You can enter it in a for loop at prompt. From your $SUBJECTS_DIR,
>  
> for subj in `ls -1`
> do
> echo "mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label --i 
> $SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum 
> $SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats"
> #mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label --i 
> $SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum 
> $SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats
> Done
>  
> I commented out the command submitting mri_segstat. I always verify the 
> printout from the echo first before submitting the jobs.
>  
> Hope this helps.
>  
> Best,
>  
> Yujing
>  
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Luke K Harper
> Sent: Friday, December 2, 2022 10:08 AM
> To: Freesurfer support list  <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] LGI label statistics
>  
> External Email - Use Caution
> 
> Hi Yujing
>  
> Ah great, Thank you so much for your help! That was the answer. I have been 
> able to extract the stats now using the following script:
>  
> mri_segstats --slabel A152 rh $SUBJECTS_DIR/A152/label/rh.c1.label --i 
> $SUBJECTS_DIR/A152/surf/rh.pial_lgi --sum 
> $SUBJECTS_DIR/A152/stats/rh.c1.pial_lgi.stats
>  
> I have 186 individuals and have been trying to extract each individuals 
> statistics individually, do you know if there is a bash shell script 
> available to perform this process on all individuals in my study at once?
>  
> Best,
> Luke
>  
>  
> 
> On 2 Dec 2022, at 15:28, Huang, Yujing  <mailto:yhuan...@mgh.harvard.edu>> wrote:
>  
> Hi Luke,
>  
> Can you try to pass the full path to your label file?  Instead of 
> ‘rh.c1.label’, pass ‘/Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label’ 
> to mri_segstats.
>  
> I think that should work.
>  
> Best,
>  
> Yujing
>  
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Luke K Harper
> Sent: Friday, December 2, 2022 5:14 AM
> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
> Subject: [Freesurfer] LGI label statistics
>  
> External Email - Use Caution
> Dear freesurfer,
>  
> I am attempting to extract LGI statistical data from a label running the 
> mri_segstats command
>  
> Here is the script I am attempting to run:
>  
> mri_segstats --slabel A152 rh rh.c1.label --i 
> $SUBJECTS_DIR/A152/surf/rh.pial_lgi --sum rh.aparc.pial_lgi.stats
>  
> This returns an error: error: mri_segstats: could not open label file 
> rh.c1.label
>  
> I created the label using freeview - make closed path - then filling the 
> closed path. The label projects on pial and inflated surfaces
> Furthermore the label is able to be identified and used in the following 
> command
>  
> mris_anatomical_stats \
> -l /Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label \
> -f /Users/lu8342ha/Desktop/subjects/A152/stats/rh.c1.stats \
> A152 \
> rh
>  
> Please could you advise me on wh

Re: [Freesurfer] LGI label statistics

Sorry, ‘Done’ should be in all lower case.

for subj in `ls -1`
do
echo "mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label --i 
$SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum 
$SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats"
#mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label --i 
$SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum 
$SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats
done

1. remove the commented out line # first to verify echo printout
2. add back the line w/o the # sign

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Huang, Yujing
Sent: Friday, December 2, 2022 10:34 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] LGI label statistics

Hi Luke,

I don’t know any bash script available to perform the batch job.

You can enter it in a for loop at prompt. From your $SUBJECTS_DIR,

for subj in `ls -1`
do
echo "mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label --i 
$SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum 
$SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats"
#mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label --i 
$SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum 
$SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats
Done

I commented out the command submitting mri_segstat. I always verify the 
printout from the echo first before submitting the jobs.

Hope this helps.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Luke K Harper
Sent: Friday, December 2, 2022 10:08 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] LGI label statistics


External Email - Use Caution
Hi Yujing

Ah great, Thank you so much for your help! That was the answer. I have been 
able to extract the stats now using the following script:

mri_segstats --slabel A152 rh $SUBJECTS_DIR/A152/label/rh.c1.label --i 
$SUBJECTS_DIR/A152/surf/rh.pial_lgi --sum 
$SUBJECTS_DIR/A152/stats/rh.c1.pial_lgi.stats

I have 186 individuals and have been trying to extract each individuals 
statistics individually, do you know if there is a bash shell script available 
to perform this process on all individuals in my study at once?

Best,
Luke


On 2 Dec 2022, at 15:28, Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:

Hi Luke,

Can you try to pass the full path to your label file?  Instead of 
‘rh.c1.label’, pass ‘/Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label’ 
to mri_segstats.

I think that should work.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Luke K Harper
Sent: Friday, December 2, 2022 5:14 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] LGI label statistics

External Email - Use Caution
Dear freesurfer,

I am attempting to extract LGI statistical data from a label running the 
mri_segstats command

Here is the script I am attempting to run:

mri_segstats --slabel A152 rh rh.c1.label --i 
$SUBJECTS_DIR/A152/surf/rh.pial_lgi --sum rh.aparc.pial_lgi.stats

This returns an error: error: mri_segstats: could not open label file 
rh.c1.label

I created the label using freeview - make closed path - then filling the closed 
path. The label projects on pial and inflated surfaces
Furthermore the label is able to be identified and used in the following command

mris_anatomical_stats \
-l /Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label \
-f /Users/lu8342ha/Desktop/subjects/A152/stats/rh.c1.stats \
A152 \
rh

Please could you advise me on where I am going wrong here?

Many thanks,

Luke
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Re: [Freesurfer] LGI label statistics

Hi Luke,

I don’t know any bash script available to perform the batch job.

You can enter it in a for loop at prompt. From your $SUBJECTS_DIR,

for subj in `ls -1`
do
echo "mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label --i 
$SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum 
$SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats"
#mri_segstats --slabel A152 rh $SUBJECTS_DIR/$subj/label/rh.c1.label --i 
$SUBJECTS_DIR/$subj/surf/rh.pial_lgi --sum 
$SUBJECTS_DIR/$subj/stats/rh.c1.pial_lgi.stats
Done

I commented out the command submitting mri_segstat. I always verify the 
printout from the echo first before submitting the jobs.

Hope this helps.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Luke K Harper
Sent: Friday, December 2, 2022 10:08 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] LGI label statistics


External Email - Use Caution
Hi Yujing

Ah great, Thank you so much for your help! That was the answer. I have been 
able to extract the stats now using the following script:

mri_segstats --slabel A152 rh $SUBJECTS_DIR/A152/label/rh.c1.label --i 
$SUBJECTS_DIR/A152/surf/rh.pial_lgi --sum 
$SUBJECTS_DIR/A152/stats/rh.c1.pial_lgi.stats

I have 186 individuals and have been trying to extract each individuals 
statistics individually, do you know if there is a bash shell script available 
to perform this process on all individuals in my study at once?

Best,
Luke



On 2 Dec 2022, at 15:28, Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> wrote:

Hi Luke,

Can you try to pass the full path to your label file?  Instead of 
‘rh.c1.label’, pass ‘/Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label’ 
to mri_segstats.

I think that should work.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Luke K Harper
Sent: Friday, December 2, 2022 5:14 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] LGI label statistics

External Email - Use Caution
Dear freesurfer,

I am attempting to extract LGI statistical data from a label running the 
mri_segstats command

Here is the script I am attempting to run:

mri_segstats --slabel A152 rh rh.c1.label --i 
$SUBJECTS_DIR/A152/surf/rh.pial_lgi --sum rh.aparc.pial_lgi.stats

This returns an error: error: mri_segstats: could not open label file 
rh.c1.label

I created the label using freeview - make closed path - then filling the closed 
path. The label projects on pial and inflated surfaces
Furthermore the label is able to be identified and used in the following command

mris_anatomical_stats \
-l /Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label \
-f /Users/lu8342ha/Desktop/subjects/A152/stats/rh.c1.stats \
A152 \
rh

Please could you advise me on where I am going wrong here?

Many thanks,

Luke
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Re: [Freesurfer] LGI label statistics

External Email - Use Caution

Hi Yujing

Ah great, Thank you so much for your help! That was the answer. I have been 
able to extract the stats now using the following script:

mri_segstats --slabel A152 rh $SUBJECTS_DIR/A152/label/rh.c1.label --i 
$SUBJECTS_DIR/A152/surf/rh.pial_lgi --sum 
$SUBJECTS_DIR/A152/stats/rh.c1.pial_lgi.stats

I have 186 individuals and have been trying to extract each individuals 
statistics individually, do you know if there is a bash shell script available 
to perform this process on all individuals in my study at once?

Best,
Luke
 

> On 2 Dec 2022, at 15:28, Huang, Yujing  wrote:
> 
> Hi Luke,
>  
> Can you try to pass the full path to your label file?  Instead of 
> ‘rh.c1.label’, pass ‘/Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label’ 
> to mri_segstats.
>  
> I think that should work.
>  
> Best,
>  
> Yujing
>  
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Luke K Harper
> Sent: Friday, December 2, 2022 5:14 AM
> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
> Subject: [Freesurfer] LGI label statistics
>  
> External Email - Use Caution
> 
> Dear freesurfer,
>  
> I am attempting to extract LGI statistical data from a label running the 
> mri_segstats command
>  
> Here is the script I am attempting to run:
>  
> mri_segstats --slabel A152 rh rh.c1.label --i 
> $SUBJECTS_DIR/A152/surf/rh.pial_lgi --sum rh.aparc.pial_lgi.stats
>  
> This returns an error: error: mri_segstats: could not open label file 
> rh.c1.label
>  
> I created the label using freeview - make closed path - then filling the 
> closed path. The label projects on pial and inflated surfaces
> Furthermore the label is able to be identified and used in the following 
> command
>  
> mris_anatomical_stats \
> -l /Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label \
> -f /Users/lu8342ha/Desktop/subjects/A152/stats/rh.c1.stats \
> A152 \
> rh
>  
> Please could you advise me on where I am going wrong here?
>  
> Many thanks,
>  
> Luke
> ___
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>  
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Re: [Freesurfer] LGI label statistics

Hi Luke,

Can you try to pass the full path to your label file?  Instead of 
'rh.c1.label', pass '/Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label' 
to mri_segstats.

I think that should work.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Luke K Harper
Sent: Friday, December 2, 2022 5:14 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] LGI label statistics


External Email - Use Caution
Dear freesurfer,

I am attempting to extract LGI statistical data from a label running the 
mri_segstats command

Here is the script I am attempting to run:

mri_segstats --slabel A152 rh rh.c1.label --i 
$SUBJECTS_DIR/A152/surf/rh.pial_lgi --sum rh.aparc.pial_lgi.stats

This returns an error: error: mri_segstats: could not open label file 
rh.c1.label

I created the label using freeview - make closed path - then filling the closed 
path. The label projects on pial and inflated surfaces
Furthermore the label is able to be identified and used in the following command

mris_anatomical_stats \
-l /Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label \
-f /Users/lu8342ha/Desktop/subjects/A152/stats/rh.c1.stats \
A152 \
rh

Please could you advise me on where I am going wrong here?

Many thanks,

Luke
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[Freesurfer] LGI label statistics

2021-08-19 Thread Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience

External Email - Use Caution

Dear freesurfer,

I am attempting to extract LGI statistical data from a label running the 
mri_segstats command

Here is the script I am attempting to run:

mri_segstats --slabel A152 rh rh.c1.label --i 
$SUBJECTS_DIR/A152/surf/rh.pial_lgi --sum rh.aparc.pial_lgi.stats

This returns an error: error: mri_segstats: could not open label file 
rh.c1.label

I created the label using freeview - make closed path - then filling the closed 
path. The label projects on pial and inflated surfaces
Furthermore the label is able to be identified and used in the following command

mris_anatomical_stats \
-l /Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label \
-f /Users/lu8342ha/Desktop/subjects/A152/stats/rh.c1.stats \
A152 \
rh

Please could you advise me on where I am going wrong here?

Many thanks,

Luke___
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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
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Re: [Freesurfer] lGI value aberrantly high, again

2022-02-04 Thread Douglas N. Greve

The lGI is run from recon-all so it is still the lGI that is the problem

On 2/1/2022 3:41 AM, Bernardoni, Fabio wrote:
>  External Email - Use Caution
>
> dear douglas
>
> thanks for your answer. I understand the developer is not maintaining the 
> program computing lGI. however, my question refers ultimately to the 
> recon-all preprocessing. I am trying to make it run again using different 
> random seed, but apparently it uses the same random seed. or am I wrong? 
> whether this rerun with a new random seed solves the lGI problem is yet to be 
> proven.
>
> thanks
>
> fabio
>
> Dr. Fabio Bernardoni
> wiss. Mitarbeiter
>
> Division of Psychological & Social Medicine and Developmental Neurosciences
> http://secure-web.cisco.com/10ROFpusm7251nd4R7VbhOMTRpfG2ZVw1NyefMENfUDi6dM90KVg1F580Ru3Y546PmS-h-yp2hhRc5_K7k433uq2EJ9eaN9s8N9_CsTS54vv8mPbTTC2nPXc9xuueUufUXY3wMTbe-X_hCg0_ZeY_3dPgUiI9Z8XB_Gj9VNMxWl_xWy1cJLx0YYY58z5B_NtHWLg0JcHnV3Bii40hBJXokL86POx5de5HjDYxX4xjuGmgmKVcOu7L97BLr6q4WUSuF41E4SlFTBFZ6U2Tm1xn9izIPo9PZQTv9aJG7uBQpIMI0PKO3sNOOljdWZHt7nV5/http%3A%2F%2Fwww.transdenlab.de%2F;
>  
> http://secure-web.cisco.com/1N4i9jIw8bJ2yyEYm19KEnx7NejoYUvpMYJhTzabx3pM9WaR339FXo0cTYTnMG39Foa8qvhVU2_8sNrquKhF4qAsTbKSG9Z0oc8FpUcbGEy7i36ukcG61fyttQYv8XXhwwxXvV3hBnHapvelFfE8Pn5pDQ0WAfV4wZFJBGhZA626M5UmsO0459TbVf4ixVsEZYfxGNenU8juB_rCXF3DaBEPluT9pyjsQE-iaDbPS2NSUkf5WLaqMg5LGErAya774gsfdaTWVSLHUYor57w1MmZSDyTiP8oZOjJpFtyyto7rDK7yUW-8sU54kPtcWm2wjmaIqnNeBo56a9qayzutOJA/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
> +49 (0351) 458-5245
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> an der Technischen Universität Dresden
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>
> Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
> Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
> USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
>
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> Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
> USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
>
> 
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>  im Auftrag von Douglas N. Greve 
> 
> Gesendet: Mittwoch, 26. Januar 2022 23:02:04
> An: freesurfer@nmr.mgh.harvard.edu
> Betreff: Re: [Freesurfer] lGI value aberrantly high, again
>
> Sorry, the developer of this program has moved on in her career so we
> have no one to support it anymore. We maybe looking at it again in the
> next year or so.
>
> On 1/25/2022 4:49 AM, Bernardoni, Fabio wrote:
>>   External Email - Use Caution
>>
>> Dear all
>>
>> as some other posted before me, sometimes the computation of lGI fails with 
>> the message
>> (see for example: 
>> https://secure-web.cisco.com/1LP2MjWSbRkQqjVjAMGGAySVoeFkdNhk1cYwhbxxVDmXiHS_3t4OH5UTR99dcG2qgX8efaQYfhcbbftI-T2HYptb4KL3ZxlJjmDP29gWStsqjsaXvuFBk4EbaR1a9qpkSEEv7T6728G9zmUkpM6YAnjA1vEPUDUxgGKRG01r5vncEqkblMdNFz83z_BWs17Fb8ykfKufUQ0xfAdSe0LltyVNpsoV8r0EqhFmBYnhc9cgJSDHJCTnacrHKTj903Cyhq_ipT6u0aXXfKPGPIywUCGjEtIJIpuB1YENqkI28eagbxGBMORYw7MZ-HDsYMxmE-9Hn6NPKsBI_SfwfFAoXqw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg09284.html,
>>  
>> https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9WeP4jQEkCEs7No1A_FAjMj-HuftunURSuN0N10wdCGoHGtBZGdUc3hRRmgwnciLVgKWNy5KLYZ3kxjxmP95hjyOoPZTfxxTflg0jrV1DDAI_8dvyMRdF4kPyU7DkdMg0Dszh18VasP42tZItX7TCxBzX98bzSpYlZwE5K_f0KVAMzrcgXoObWgHQ6AAzgmTxZ3iuxfkHadgKf1VMNkhheh6LWpdrPfewMYwN6ElTUiBM2Wd74K2w7Ni6J6qOIAA12IIN_nR_OXnKgZsh0MUN5b3RYmgVd6T3csf34S-Og/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg44781.html,
>>  
>> https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9WeP4jQEkCEs7No1A_FAjMj-HuftunURSuN0N10wdCGoHGtBZGdUc3hRRmgwnciLVgKWNy5KLYZ3kxjxmP95hjyOoPZTfxxTflg0jrV1DDAI_8dvyMRdF4kPyU7DkdMg0Dszh18VasP42tZItX7TCxBzX98bzSpYlZwE5K_

Re: [Freesurfer] lGI value aberrantly high, again

2022-02-01 Thread Bernardoni, Fabio

External Email - Use Caution

dear douglas

thanks for your answer. I understand the developer is not maintaining the 
program computing lGI. however, my question refers ultimately to the recon-all 
preprocessing. I am trying to make it run again using different random seed, 
but apparently it uses the same random seed. or am I wrong? whether this rerun 
with a new random seed solves the lGI problem is yet to be proven.

thanks

fabio

Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/10ROFpusm7251nd4R7VbhOMTRpfG2ZVw1NyefMENfUDi6dM90KVg1F580Ru3Y546PmS-h-yp2hhRc5_K7k433uq2EJ9eaN9s8N9_CsTS54vv8mPbTTC2nPXc9xuueUufUXY3wMTbe-X_hCg0_ZeY_3dPgUiI9Z8XB_Gj9VNMxWl_xWy1cJLx0YYY58z5B_NtHWLg0JcHnV3Bii40hBJXokL86POx5de5HjDYxX4xjuGmgmKVcOu7L97BLr6q4WUSuF41E4SlFTBFZ6U2Tm1xn9izIPo9PZQTv9aJG7uBQpIMI0PKO3sNOOljdWZHt7nV5/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/1N4i9jIw8bJ2yyEYm19KEnx7NejoYUvpMYJhTzabx3pM9WaR339FXo0cTYTnMG39Foa8qvhVU2_8sNrquKhF4qAsTbKSG9Z0oc8FpUcbGEy7i36ukcG61fyttQYv8XXhwwxXvV3hBnHapvelFfE8Pn5pDQ0WAfV4wZFJBGhZA626M5UmsO0459TbVf4ixVsEZYfxGNenU8juB_rCXF3DaBEPluT9pyjsQE-iaDbPS2NSUkf5WLaqMg5LGErAya774gsfdaTWVSLHUYor57w1MmZSDyTiP8oZOjJpFtyyto7rDK7yUW-8sU54kPtcWm2wjmaIqnNeBo56a9qayzutOJA/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://secure-web.cisco.com/16eVZdzuQm5qbm80qB8dztwMp6QFUkUZ0nFXE37Ypqc4REnOQM7fTSV13LSRRhFWKc7YOcgyF0u1v7WIS8StfxEqbSN1QZUB9W2l4c7t1Qjas9CpbS75zCrZj0nqO9wQo1_jIv8sdZpBYG5Y1bbDLqV993EdxHEWToOzJwKgqdHpSke8vqy6Xb93g_c4PgqGddOT6YXhMcGMWHr4f9WiF1Ur3FSvlMm4ALJZ4-uD5xvcTpf1A4-M_hhU9Jgj6nZWlkthGy2DPSFOcnC9sf_c205y0GHfslg0VbOZS240aXVnYwiTgl0QUCS7nqox8rL4XWbMGuswgO1Se9lRBxjP-Xg/http%3A%2F%2Fwww.uniklinikum-dresden.de

Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

http://secure-web.cisco.com/16eVZdzuQm5qbm80qB8dztwMp6QFUkUZ0nFXE37Ypqc4REnOQM7fTSV13LSRRhFWKc7YOcgyF0u1v7WIS8StfxEqbSN1QZUB9W2l4c7t1Qjas9CpbS75zCrZj0nqO9wQo1_jIv8sdZpBYG5Y1bbDLqV993EdxHEWToOzJwKgqdHpSke8vqy6Xb93g_c4PgqGddOT6YXhMcGMWHr4f9WiF1Ur3FSvlMm4ALJZ4-uD5xvcTpf1A4-M_hhU9Jgj6nZWlkthGy2DPSFOcnC9sf_c205y0GHfslg0VbOZS240aXVnYwiTgl0QUCS7nqox8rL4XWbMGuswgO1Se9lRBxjP-Xg/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Douglas N. Greve 

Gesendet: Mittwoch, 26. Januar 2022 23:02:04
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] lGI value aberrantly high, again

Sorry, the developer of this program has moved on in her career so we
have no one to support it anymore. We maybe looking at it again in the
next year or so.

On 1/25/2022 4:49 AM, Bernardoni, Fabio wrote:
>  External Email - Use Caution
>
> Dear all
>
> as some other posted before me, sometimes the computation of lGI fails with 
> the message
> (see for example: 
> https://secure-web.cisco.com/1LP2MjWSbRkQqjVjAMGGAySVoeFkdNhk1cYwhbxxVDmXiHS_3t4OH5UTR99dcG2qgX8efaQYfhcbbftI-T2HYptb4KL3ZxlJjmDP29gWStsqjsaXvuFBk4EbaR1a9qpkSEEv7T6728G9zmUkpM6YAnjA1vEPUDUxgGKRG01r5vncEqkblMdNFz83z_BWs17Fb8ykfKufUQ0xfAdSe0LltyVNpsoV8r0EqhFmBYnhc9cgJSDHJCTnacrHKTj903Cyhq_ipT6u0aXXfKPGPIywUCGjEtIJIpuB1YENqkI28eagbxGBMORYw7MZ-HDsYMxmE-9Hn6NPKsBI_SfwfFAoXqw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg09284.html,
>  
> https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9WeP4jQEkCEs7No1A_FAjMj-HuftunURSuN0N10wdCGoHGtBZGdUc3hRRmgwnciLVgKWNy5KLYZ3kxjxmP95hjyOoPZTfxxTflg0jrV1DDAI_8dvyMRdF4kPyU7DkdMg0Dszh18VasP42tZItX7TCxBzX98bzSpYlZwE5K_f0KVAMzrcgXoObWgHQ6AAzgmTxZ3iuxfkHadgKf1VMNkhheh6LWpdrPfewMYwN6ElTUiBM2Wd74K2w7Ni6J6qOIAA12IIN_nR_OXnKgZsh0MUN5b3RYmgVd6T3csf34S-Og/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg44781.html,
>  
> https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9WeP4jQEkCEs7No1A_FAjMj-HuftunURSuN0N10wdCGoHGtBZGdUc3hRRmgwnciLVgKWNy5KLYZ3kxjxmP95hjyOoPZTfxxTflg0jrV1DDAI_8dvyMRdF4kPyU7DkdMg0Dszh18VasP42tZItX7TCxBzX98bzSpYlZwE5K_f0KVAMzrcgXoObWgHQ6AAzgmTxZ3iuxfkHadgKf1VMNkhheh6LWpdrPfewMYwN6ElTUiBM2Wd74K2w7Ni6J6qOIAA12IIN_nR_OXnKgZsh0MUN5b3RYmgVd6T3csf34S-Og/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg44781.html)
>
> 'lGI for vertex number 35901 of the outer mesh is 2.5958
> ... remeasuring lGI value for vertex iV = 36001. It may take a few minutes.
> WARNING -- Problem for vertex iV =

Re: [Freesurfer] lGI value aberrantly high, again

2022-01-26 Thread Douglas N. Greve

Sorry, the developer of this program has moved on in her career so we 
have no one to support it anymore. We maybe looking at it again in the 
next year or so.

On 1/25/2022 4:49 AM, Bernardoni, Fabio wrote:
>  External Email - Use Caution
>
> Dear all
>
> as some other posted before me, sometimes the computation of lGI fails with 
> the message
> (see for example: 
> https://secure-web.cisco.com/1LP2MjWSbRkQqjVjAMGGAySVoeFkdNhk1cYwhbxxVDmXiHS_3t4OH5UTR99dcG2qgX8efaQYfhcbbftI-T2HYptb4KL3ZxlJjmDP29gWStsqjsaXvuFBk4EbaR1a9qpkSEEv7T6728G9zmUkpM6YAnjA1vEPUDUxgGKRG01r5vncEqkblMdNFz83z_BWs17Fb8ykfKufUQ0xfAdSe0LltyVNpsoV8r0EqhFmBYnhc9cgJSDHJCTnacrHKTj903Cyhq_ipT6u0aXXfKPGPIywUCGjEtIJIpuB1YENqkI28eagbxGBMORYw7MZ-HDsYMxmE-9Hn6NPKsBI_SfwfFAoXqw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg09284.html,
>  
> https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9WeP4jQEkCEs7No1A_FAjMj-HuftunURSuN0N10wdCGoHGtBZGdUc3hRRmgwnciLVgKWNy5KLYZ3kxjxmP95hjyOoPZTfxxTflg0jrV1DDAI_8dvyMRdF4kPyU7DkdMg0Dszh18VasP42tZItX7TCxBzX98bzSpYlZwE5K_f0KVAMzrcgXoObWgHQ6AAzgmTxZ3iuxfkHadgKf1VMNkhheh6LWpdrPfewMYwN6ElTUiBM2Wd74K2w7Ni6J6qOIAA12IIN_nR_OXnKgZsh0MUN5b3RYmgVd6T3csf34S-Og/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg44781.html,
>  
> https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9WeP4jQEkCEs7No1A_FAjMj-HuftunURSuN0N10wdCGoHGtBZGdUc3hRRmgwnciLVgKWNy5KLYZ3kxjxmP95hjyOoPZTfxxTflg0jrV1DDAI_8dvyMRdF4kPyU7DkdMg0Dszh18VasP42tZItX7TCxBzX98bzSpYlZwE5K_f0KVAMzrcgXoObWgHQ6AAzgmTxZ3iuxfkHadgKf1VMNkhheh6LWpdrPfewMYwN6ElTUiBM2Wd74K2w7Ni6J6qOIAA12IIN_nR_OXnKgZsh0MUN5b3RYmgVd6T3csf34S-Og/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg44781.html)
>
> 'lGI for vertex number 35901 of the outer mesh is 2.5958
> ... remeasuring lGI value for vertex iV = 36001. It may take a few minutes.
> WARNING -- Problem for vertex iV = 36001, lGI value is aberrantly high 
> (lGI=53.1127)...
> ...lGI computation will be stopped. This may be caused by topological 
> defects, check mris_euler_number on the pial surface.'
>
> as many reported before me, computation of euler number gives 2, i.e. nothing 
> wrong. another suggestion by marie schaer is to
> rerun recon-all -hemi ?h -autorecon2 -autorecon3 , with or without the 
> -randomness option.
>
> The point is that the -randomness option seems to have no effect, the error 
> occurs again in exactly the same place, with the exact same value 
> (lGI=53.1127).
>
> I am using freesurfer 7.1. Has there been any development to solve this?
>
> Thank you in advance
>
> Fabio Bernardoni
>
>
> Dr. Fabio Bernardoni
> wiss. Mitarbeiter
>
> Division of Psychological & Social Medicine and Developmental Neurosciences
> http://secure-web.cisco.com/1xvuU9YpZrNAT8MBR8aeslCWdv2cNu-xhctWukMA-pgRDlfQq65obryki5fZ9inqQJGhUQCH12N3Pt0ACl5Sz6LbLbSEiQUG8WQO9t88xjEbBwfnJl5zMPv5YGf2um_2huADEEKMstPPgZ-2NbXimHQPHK5qCSvFMpSsGruW0svSkAaRlYlbli_Lh272QlD4J26lfLiQzwTVCqVKRna8BCUGR8yVWddr_LDg_XEqia5dNbzYZDkwnUBTG2F9ISpoIXh3TOciVMBbhbfFjq4oyGcs3f8IYSIi2hIbnpM9C-K7UBqfq6JgC8MOXudQm7m45/http%3A%2F%2Fwww.transdenlab.de%2F;
>  
> http://secure-web.cisco.com/18N9590xMz7PXy9R7etuq98MdgjKagN7Y04h0saKn6vRWYJ38YRbvIQam95p0_9OaNAtoH0qHBY20t69GRnCZNTRBEMY7L0dD_0kA9XSvn1emw5Cg068ZJTAc2rajYXBSywtHWwSBJv5Bk3AMNCwDT208lNW5A1KBEHxU6ClKWG0biFGmUlIMeH8DzBxdhTFSc46EnzdD9atOQtFO8_qTgvGgNFOhfvwKS67YeTzV4Q22C-y953EVIfJo84NUaLXgIRwlO-_erSBNdJlV-6iBgXbIA2PkyekWYcjKAGknDwCZ9FeDCXXrfPaTjhOLpleBfcBwLPTaoDD3w_UZqZxxZw/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
> +49 (0351) 458-5245
> Universitätsklinikum Carl Gustav Carus
> an der Technischen Universität Dresden
> Anstalt des öffentlichen Rechts des Freistaates Sachsen
> Fetscherstraße 74, 01307 Dresden
> http://secure-web.cisco.com/108KZKatqumySxQAcQhTRI4pLm-1UWBgP9aUo19kQxHoswPNbN5Y93CIS1m_AZYvI5g89xt3D8fWeG-nZGHcWIQwdgK8LBVhodCmEXFq0EKDBLAsOIVvTG4LeWM5r8y2JLCZ2mOd9g9GLcMjVMjeQjD5VgJU5LeAZNm-NJ5tBPB1hF8wvnJNJ2X2cLJ5vZKLU2aYgxN-WuZE1cGjXWay2opcuDq7SitYKNWvlz762MMOCM8bMv3z8ZWoGK9BOsPrEDz0rsK0tuSSiFgl7gEIb24bX2LfSiWILL6YaWrYsO3oymz8wM88PTz3iRsLfW82BhTXKtAPLBEvL3og_vVMoTA/http%3A%2F%2Fwww.uniklinikum-dresden.de
>
> Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
> Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
> USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
>
> http://secure-web.cisco.com/108KZKatqumySxQAcQhTRI4pLm-1UWBgP9aUo19kQxHoswPNbN5Y93CIS1m_AZYvI5g89xt3D8fWeG-nZGHcWIQwdgK8LBVhodCmEXFq0EKDBLAsOIVvTG4LeWM5r8y2JLCZ2mOd9g9GLcMjVMjeQjD5VgJU5LeAZNm-NJ5tBPB1hF8wvnJNJ2X2cLJ5vZKLU2aYgxN-WuZE1cGjXWay2opcuDq7SitYKNWvlz762MMOCM8bMv3z8ZWoGK9BOsPrEDz0rsK0tuSSiFgl7gEIb24bX2LfSiWILL6YaWrYsO3oymz8wM88PTz3iRsLfW82BhTXKtAPLBEvL3og_vVMoTA/http%3A%2F%2Fwww.uniklinikum-dresden.de
> Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
> Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
> USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
>
>
>

[Freesurfer] lGI value aberrantly high, again

2022-01-25 Thread Bernardoni, Fabio

External Email - Use Caution

Dear all

as some other posted before me, sometimes the computation of lGI fails with the
message
(see for example:
https://secure-web.cisco.com/1LP2MjWSbRkQqjVjAMGGAySVoeFkdNhk1cYwhbxxVDmXiHS_3t4OH5UTR99dcG2qgX8efaQYfhcbbftI-T2HYptb4KL3ZxlJjmDP29gWStsqjsaXvuFBk4EbaR1a9qpkSEEv7T6728G9zmUkpM6YAnjA1vEPUDUxgGKRG01r5vncEqkblMdNFz83z_BWs17Fb8ykfKufUQ0xfAdSe0LltyVNpsoV8r0EqhFmBYnhc9cgJSDHJCTnacrHKTj903Cyhq_ipT6u0aXXfKPGPIywUCGjEtIJIpuB1YENqkI28eagbxGBMORYw7MZ-HDsYMxmE-9Hn6NPKsBI_SfwfFAoXqw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg09284.html,

https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9WeP4jQEkCEs7No1A_FAjMj-HuftunURSuN0N10wdCGoHGtBZGdUc3hRRmgwnciLVgKWNy5KLYZ3kxjxmP95hjyOoPZTfxxTflg0jrV1DDAI_8dvyMRdF4kPyU7DkdMg0Dszh18VasP42tZItX7TCxBzX98bzSpYlZwE5K_f0KVAMzrcgXoObWgHQ6AAzgmTxZ3iuxfkHadgKf1VMNkhheh6LWpdrPfewMYwN6ElTUiBM2Wd74K2w7Ni6J6qOIAA12IIN_nR_OXnKgZsh0MUN5b3RYmgVd6T3csf34S-Og/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg44781.html,

'lGI for vertex number 35901 of the outer mesh is 2.5958
... remeasuring lGI value for vertex iV = 36001. It may take a few minutes.
WARNING -- Problem for vertex iV = 36001, lGI value is aberrantly high
(lGI=53.1127)...
...lGI computation will be stopped. This may be caused by topological defects,
check mris_euler_number on the pial surface.'

as many reported before me, computation of euler number gives 2, i.e. nothing
wrong. another suggestion by marie schaer is to
rerun recon-all -hemi ?h -autorecon2 -autorecon3 , with or without the
-randomness option.

The point is that the -randomness option seems to have no effect, the error
occurs again in exactly the same place, with the exact same value
(lGI=53.1127).

I am using freesurfer 7.1. Has there been any development to solve this?

Thank you in advance

Fabio Bernardoni

Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1xvuU9YpZrNAT8MBR8aeslCWdv2cNu-xhctWukMA-pgRDlfQq65obryki5fZ9inqQJGhUQCH12N3Pt0ACl5Sz6LbLbSEiQUG8WQO9t88xjEbBwfnJl5zMPv5YGf2um_2huADEEKMstPPgZ-2NbXimHQPHK5qCSvFMpSsGruW0svSkAaRlYlbli_Lh272QlD4J26lfLiQzwTVCqVKRna8BCUGR8yVWddr_LDg_XEqia5dNbzYZDkwnUBTG2F9ISpoIXh3TOciVMBbhbfFjq4oyGcs3f8IYSIi2hIbnpM9C-K7UBqfq6JgC8MOXudQm7m45/http%3A%2F%2Fwww.transdenlab.de%2F;

http://secure-web.cisco.com/18N9590xMz7PXy9R7etuq98MdgjKagN7Y04h0saKn6vRWYJ38YRbvIQam95p0_9OaNAtoH0qHBY20t69GRnCZNTRBEMY7L0dD_0kA9XSvn1emw5Cg068ZJTAc2rajYXBSywtHWwSBJv5Bk3AMNCwDT208lNW5A1KBEHxU6ClKWG0biFGmUlIMeH8DzBxdhTFSc46EnzdD9atOQtFO8_qTgvGgNFOhfvwKS67YeTzV4Q22C-y953EVIfJo84NUaLXgIRwlO-_erSBNdJlV-6iBgXbIA2PkyekWYcjKAGknDwCZ9FeDCXXrfPaTjhOLpleBfcBwLPTaoDD3w_UZqZxxZw/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://secure-web.cisco.com/108KZKatqumySxQAcQhTRI4pLm-1UWBgP9aUo19kQxHoswPNbN5Y93CIS1m_AZYvI5g89xt3D8fWeG-nZGHcWIQwdgK8LBVhodCmEXFq0EKDBLAsOIVvTG4LeWM5r8y2JLCZ2mOd9g9GLcMjVMjeQjD5VgJU5LeAZNm-NJ5tBPB1hF8wvnJNJ2X2cLJ5vZKLU2aYgxN-WuZE1cGjXWay2opcuDq7SitYKNWvlz762MMOCM8bMv3z8ZWoGK9BOsPrEDz0rsK0tuSSiFgl7gEIb24bX2LfSiWILL6YaWrYsO3oymz8wM88PTz3iRsLfW82BhTXKtAPLBEvL3og_vVMoTA/http%3A%2F%2Fwww.uniklinikum-dresden.de

Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

http://secure-web.cisco.com/108KZKatqumySxQAcQhTRI4pLm-1UWBgP9aUo19kQxHoswPNbN5Y93CIS1m_AZYvI5g89xt3D8fWeG-nZGHcWIQwdgK8LBVhodCmEXFq0EKDBLAsOIVvTG4LeWM5r8y2JLCZ2mOd9g9GLcMjVMjeQjD5VgJU5LeAZNm-NJ5tBPB1hF8wvnJNJ2X2cLJ5vZKLU2aYgxN-WuZE1cGjXWay2opcuDq7SitYKNWvlz762MMOCM8bMv3z8ZWoGK9BOsPrEDz0rsK0tuSSiFgl7gEIb24bX2LfSiWILL6YaWrYsO3oymz8wM88PTz3iRsLfW82BhTXKtAPLBEvL3og_vVMoTA/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

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Re: [Freesurfer] LGI - output issue

External Email - Use Caution

It worked! Thank you so much for fixing this.

I am also trying to open ?h.pial-outer-smoothed file. How should I proceed
with either freeview or tksurferfv? Haven't found any info regarding this
on the wiki!

Again, thank you so much for your help!

All the best

On Wed, Aug 18, 2021 at 11:37 PM Hoopes, Andrew 
wrote:

> This is fixed in v7.2, but if you want to patch your current freesurfer
> distribution, you can try these commands:
>
>
>
> cd $FREESURFER_HOME/bin
>
> sudo mv fsvglrun fsvglrun.backup
>
> sudo curl -O
> https://secure-web.cisco.com/1efCCkX86LzSzP4WTrfKmXAn_UMOkClX1vXHyTzq468M8EqFH6ADhRk-mxvzBUdRYKoD8cdJjHKHVpbGLvr1uJiv3c7wTqLU-GD6Czs0AnxCjEJXuXNtKD9i6EYVGk_5daCrvcj9RAllhwgE15SPG3uUcTVERP5m-_ty2zGGaJ_PZHHHqJP70yt9mFG0UoB2up0mAc2y22KCUNbKW2re-1lKZO-mgyuYeie7b2Aug1Hc1_zYNLqi8EHQ2nvmJXDb_zTDo8kiPf5uDKK1lNlWO7g/https%3A%2F%2Fraw.githubusercontent.com%2Ffreesurfer%2Ffreesurfer%2Fdev%2Fscripts%2Ffsvglrun
>
> sudo chmod +x fsvglrun
>
>
>
> best
>
> Andrew
>
>
>
> *From: *freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lab of Autism and
> Developmental Neuroscience, Lab of Autism and Developmental Neuroscience <
> l...@email.gwu.edu>
> *Date: *Tuesday, August 17, 2021 at 2:43 PM
> *To: *Freesurfer support list 
> *Subject: *[Freesurfer] LGI - output issue
>
> *External Email - Use Caution*
>
> Good afternoon FreeSurfer experts,
>
>
>
> Hope that everyone is well and staying safe!
>
>
>
> I tried opening LGI freeview (or tksurferfv) output, and I have been
> running into the following issues (see code and error message outputs
> below). Any ideas how I could fix this? Please let me know if additional
> details are needed.
>
>
>
> Bolded code is what I inserted. Outputs are not bolded.
>
>
>
> *tksurfer HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi*
>
> zsh: command not found: tksurfer
>
> *tksurferfv HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi*
>
> ERROR: cannot find lh.pial_lgi
>
> *cd $SUBJECTS_DIR/HAR30303_srs2_2/surf*
>
> *tksurferfv HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi*
>
> freeview -f
> /Applications/ace_complete/HAR30303_srs2_2/surf/lh.inflated:curvature=/Applications/ace_complete/HAR30303_srs2_2/surf/lh.curv:overlay=lh.pial_lgi:overlay_threshold=2,2,5
> -viewport 3d
>
> /Applications/freesurfer/bin/fsvglrun: line 20: conditional binary
> operator expected
>
> /Applications/freesurfer/bin/fsvglrun: line 20: syntax error near
> `FS_ALLOW_VGLRUN'
>
> /Applications/freesurfer/bin/fsvglrun: line 20: `if [[ ! -v
> FS_ALLOW_VGLRUN ]]; then'
>
>
>
> Also within the surf folder, I tried something like: *freesurfer -v
> lh.pial_lgi*
>
> Output in freeview was just a dark screen - tried changing the color map
> but nothing improved this issue.
>
>
>
> Thank you so much!
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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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
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>  . If the e-mail was sent
> to you in error but does not contain patient information, please contact
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Re: [Freesurfer] LGI - output issue

2021-08-18 Thread Hoopes, Andrew

This is fixed in v7.2, but if you want to patch your current freesurfer 
distribution, you can try these commands:

cd $FREESURFER_HOME/bin
sudo mv fsvglrun fsvglrun.backup
sudo curl -O 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fsvglrun
sudo chmod +x fsvglrun

best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lab of Autism and 
Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 

Date: Tuesday, August 17, 2021 at 2:43 PM
To: Freesurfer support list 
Subject: [Freesurfer] LGI - output issue

External Email - Use Caution
Good afternoon FreeSurfer experts,

Hope that everyone is well and staying safe!

I tried opening LGI freeview (or tksurferfv) output, and I have been running 
into the following issues (see code and error message outputs below). Any ideas 
how I could fix this? Please let me know if additional details are needed.

Bolded code is what I inserted. Outputs are not bolded.

tksurfer HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi
zsh: command not found: tksurfer
tksurferfv HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi
ERROR: cannot find lh.pial_lgi
cd $SUBJECTS_DIR/HAR30303_srs2_2/surf
tksurferfv HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi
freeview -f 
/Applications/ace_complete/HAR30303_srs2_2/surf/lh.inflated:curvature=/Applications/ace_complete/HAR30303_srs2_2/surf/lh.curv:overlay=lh.pial_lgi:overlay_threshold=2,2,5
 -viewport 3d
/Applications/freesurfer/bin/fsvglrun: line 20: conditional binary operator 
expected
/Applications/freesurfer/bin/fsvglrun: line 20: syntax error near 
`FS_ALLOW_VGLRUN'
/Applications/freesurfer/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN ]]; 
then'

Also within the surf folder, I tried something like: freesurfer -v lh.pial_lgi
Output in freeview was just a dark screen - tried changing the color map but 
nothing improved this issue.

Thank you so much!


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Re: [Freesurfer] LGI - trouble creating output file for each subject

2021-08-17 Thread Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience

External Email - Use Caution

Dear Dr. Douglas,

Thank you so much for your response. I just checked in the surf folder of
this specific subject and yes, rh.white does exist. Not 100% sure how to
check if it's readable for freesurfer - could you please explain? Thank
you!

On Tue, Aug 17, 2021 at 5:45 PM Douglas N. Greve 
wrote:

> It says that it cannot find
> /Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.white
> does that file exist and readable?
>
> On 8/17/2021 5:12 PM, Lab of Autism and Developmental Neuroscience, Lab of
> Autism and Developmental Neuroscience wrote:
>
> External Email - Use Caution
> Hello again FreeSurfer experts,
>
> I am having some issues creating the output file with the LGI data for
> each subject. Could you please help me with this? See below the code (in
> bold) that I used and the outputs that I got. Please let me know if you
> need additional information!
>
> *mri_segstats --annot DCNL-fBMI-001_Siemens_MPRAGE rh aparc --i
> $SUBJECTS_DIR/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.pial_lgi --sum
> rh.DCNL_001_aparc.pial_lgi.stats*
> 7.1.0
> cwd
> cmdline mri_segstats --annot DCNL-fBMI-001_Siemens_MPRAGE rh aparc --i
> /Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.pial_lgi
> --sum rh.DCNL_001_aparc.pial_lgi.stats
> sysname  Darwin
> hostname CCAPSY-0GYM0XV
> machine  x86_64
> user ajobsaid
> whitesurfname  white
> UseRobust  0
> Constructing seg from annotation
> error: No such file or directory
> error:
> MRISread(/Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.white):
> could not open file
>
> The lh or rh.pial_lgi file is located in the surf folder in each subject.
> Should I transfer them to the stats folder and try something like 
> *asegstats2table
> -s subjectID --statsfile=rh.pial_lgi --meas mean --tablefile
> SubjectID_rh_lgi_final.txt ? *
>
> Thank you so much!!
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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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 Mass General
> Brigham Compliance HelpLine at
> http://secure-web.cisco.com/1jTZoWxS_YLhTSE13gn9KJXUGwklxPXiEBh53eZWeDPbF_PTL2LhjF69arNoKNtEF5zCj5ts7kriR6j0KZqMarNCNvMPr6y-Jr1rFKkcwX_dNx9o5iKd1x3BT_xuZI_HOz5GMIhnsvkeViA2PYUGRpEx66JYdCnglDyh94CZIf1BAuEL8BZEP6w1fUXNpLhJgp8i2EpM60LGVyvP8xOZfSQTyTNprAAntZqdt_iVGIt-xvKD1jyamVDE_cwBxRf36zYC5kAMBVNJwOrE-yAfK3A/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  . 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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> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
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Re: [Freesurfer] LGI - trouble creating output file for each subject

2021-08-17 Thread Douglas N. Greve

It says that it cannot find 
/Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.white

does that file exist and readable?

On 8/17/2021 5:12 PM, Lab of Autism and Developmental Neuroscience, Lab 
of Autism and Developmental Neuroscience wrote:


External Email - Use Caution

Hello again FreeSurfer experts,

I am having some issues creating the output file with the LGI data for 
each subject. Could you please help me with this? See below the code 
(in bold) that I used and the outputs that I got. Please let me know 
if you need additional information!


*mri_segstats --annot DCNL-fBMI-001_Siemens_MPRAGE rh aparc --i 
$SUBJECTS_DIR/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.pial_lgi --sum 
rh.DCNL_001_aparc.pial_lgi.stats*

7.1.0
cwd
cmdline mri_segstats --annot DCNL-fBMI-001_Siemens_MPRAGE rh aparc --i 
/Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.pial_lgi 
--sum rh.DCNL_001_aparc.pial_lgi.stats

sysname  Darwin
hostname CCAPSY-0GYM0XV
machine  x86_64
user     ajobsaid
whitesurfname  white
UseRobust  0
Constructing seg from annotation
error: No such file or directory
error: 
MRISread(/Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.white): 
could not open file


The lh or rh.pial_lgi file is located in the surf folder in each 
subject. Should I transfer them to the stats folder and try something 
like *asegstats2table -s subjectID --statsfile=rh.pial_lgi --meas mean 
--tablefile SubjectID_rh_lgi_final.txt ? *

*
*
Thank you so much!!

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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 Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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this message immediately.  Continuing to send or respond to e-mail after 
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continue to communicate over unencrypted e-mail.

[Freesurfer] LGI - trouble creating output file for each subject

2021-08-17 Thread Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience

External Email - Use Caution

Hello again FreeSurfer experts,

I am having some issues creating the output file with the LGI data for each
subject. Could you please help me with this? See below the code (in bold)
that I used and the outputs that I got. Please let me know if you need
additional information!

*mri_segstats --annot DCNL-fBMI-001_Siemens_MPRAGE rh aparc --i
$SUBJECTS_DIR/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.pial_lgi --sum
rh.DCNL_001_aparc.pial_lgi.stats*
7.1.0
cwd
cmdline mri_segstats --annot DCNL-fBMI-001_Siemens_MPRAGE rh aparc --i
/Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.pial_lgi
--sum rh.DCNL_001_aparc.pial_lgi.stats
sysname  Darwin
hostname CCAPSY-0GYM0XV
machine  x86_64
user ajobsaid
whitesurfname  white
UseRobust  0
Constructing seg from annotation
error: No such file or directory
error:
MRISread(/Applications/freesurfer/subjects/DCNL-fBMI-001_Siemens_MPRAGE/surf/rh.white):
could not open file

The lh or rh.pial_lgi file is located in the surf folder in each subject.
Should I transfer them to the stats folder and try something like
*asegstats2table
-s subjectID --statsfile=rh.pial_lgi --meas mean --tablefile
SubjectID_rh_lgi_final.txt ? *

Thank you so much!!
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[Freesurfer] LGI - output issue

2021-08-17 Thread Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience

External Email - Use Caution

Good afternoon FreeSurfer experts,

Hope that everyone is well and staying safe!

I tried opening LGI freeview (or tksurferfv) output, and I have been
running into the following issues (see code and error message outputs
below). Any ideas how I could fix this? Please let me know if additional
details are needed.

Bolded code is what I inserted. Outputs are not bolded.

*tksurfer HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi*
zsh: command not found: tksurfer
*tksurferfv HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi*
ERROR: cannot find lh.pial_lgi
*cd $SUBJECTS_DIR/HAR30303_srs2_2/surf*
*tksurferfv HAR30303_srs2_2 lh inflated -overlay lh.pial_lgi*
freeview -f
/Applications/ace_complete/HAR30303_srs2_2/surf/lh.inflated:curvature=/Applications/ace_complete/HAR30303_srs2_2/surf/lh.curv:overlay=lh.pial_lgi:overlay_threshold=2,2,5
-viewport 3d
/Applications/freesurfer/bin/fsvglrun: line 20: conditional binary operator
expected
/Applications/freesurfer/bin/fsvglrun: line 20: syntax error near
`FS_ALLOW_VGLRUN'
/Applications/freesurfer/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN
]]; then'

Also within the surf folder, I tried something like: *freesurfer -v
lh.pial_lgi*
Output in freeview was just a dark screen - tried changing the color map
but nothing improved this issue.

Thank you so much!
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Re: [Freesurfer] LGI FS 7.1

2021-07-11 Thread Douglas N. Greve

I'm not sure either. I don't really use lgi. Look at some of the papers 
that have and see what they do


On 7/9/2021 4:03 PM, Del Re, Elisabetta wrote:


External Email - Use Caution

External Email - Use Caution

Would you normalize for differences in head size by adjusting for eTiV 
or total surface area?

Thank you so much,
Elisabetta

Sent from my iPhone

On Jul 9, 2021, at 2:08 PM, Douglas N. Greve  
wrote:


I'm not sure what you mean. Can you elaborate?

On 6/30/2021 5:05 PM, Del Re, Elisabetta wrote:


External Email - Use Caution

External Email - Use Caution

Thank you so much.
I am still in doubt as to whether adjust/normalize for brain volume 
or otherwise surface area before comparing groups.

Thank you for your advise,
best wishes,
Elisabetta

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. 
Greve 

*Sent:* Sunday, June 20, 2021 10:34 AM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] LGI FS 7.1
The biggest changes are intensity normalization and highres support, 
but many more changes. See the release notes
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes 
<https://secure-web.cisco.com/1-zy4xnoTVIUZYOAGhBIwlDn1MFRhAABHpitnpF8oWCmzvLodj7YweHxCi0AfJBEH9aGoVZdZVRRRC-4D4E-udWSQwUBkUzi31DT_ibnUWLifKSxG2_jKz0oHC74LIelR9Ruiw5HqkQ8AC-EFFm5U9JNpwxT6MIidMgg7aGi47AOu9Spu4uA-ZhgVyGb6rEWjDtGmhEzDtp5x10ixtqWDogjgI5JjigC-V0KLODa7pucpNXiWccdKP8ahWps69nZ3pDaWwTVgCrw3-MrAes3DPw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1xB0JoEP4-2DfG6EBFVYpZNgm-5FwWEEh-2DA2gLPM-2DxdJP5exIJKbf7w6aDNPwqYmKJIR8SrNy1xr6DJo9iYqEnbwjCYfUyZQRlY8Hd4MU-2Dd6yggFqQmT66AdhaeuTQeUQ7AkgibL7x5UqcEljyQL1RT0KBiyOnReezLP4Z8-2D-2DPU2iDuGic9cXeEnro0Xpv-2DTzp6NbIfk6obBLB7iAzGhkhUqZQGiUVwZGVeRjVT6zSrZjqVvuMa21nIKQ6S9MLRSvddGz9Fo4YxwtSgSSaqFZhiC6qQ_https-253A-252F-252Fsurfer.nmr.mgh.harvard.edu-252Ffswiki-252FReleaseNotes%26d%3DDwMG-g%26c%3DWO-RGvefibhHBZq3fL85hQ%26r%3DKlJbht4h1i6aPJHMk7qSgoiYID4UiBhKWpU1g8jq1jE%26m%3DO-lvAE2GmOPl5T6lDiVcDd_ArIQ66F2bQB3zRHG9M0U%26s%3DQO-OQ-HY9n1HytwwLnLtCUEjWUs_ImrL4fw5OiuJjhs%26e%3D>



On 6/9/2021 10:17 AM, Del Re, Elisabetta wrote:


External Email - Use Caution

External Email - Use Caution


Dear FS team,
what are differences if any between LGI in FS 5.3 and 7.1?
Thank you so much,
best wishes,
Elisabetta

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Re: [Freesurfer] LGI FS 7.1

2021-07-09 Thread Del Re, Elisabetta

External Email - Use Caution

Would you normalize for differences in head size by adjusting for eTiV or total 
surface area?
Thank you so much,
Elisabetta

Sent from my iPhone

On Jul 9, 2021, at 2:08 PM, Douglas N. Greve  wrote:

 I'm not sure what you mean. Can you elaborate?

On 6/30/2021 5:05 PM, Del Re, Elisabetta wrote:

External Email - Use Caution

External Email - Use Caution

Thank you so much.
I am still in doubt as to whether adjust/normalize for brain volume or 
otherwise surface area before comparing groups.
Thank you for your advise,
best wishes,
Elisabetta

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Sent: Sunday, June 20, 2021 10:34 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] LGI FS 7.1

The biggest changes are intensity normalization and highres support, but many 
more changes. See the release notes
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On 6/9/2021 10:17 AM, Del Re, Elisabetta wrote:

External Email - Use Caution

External Email - Use Caution

Dear FS team,
what are differences if any between LGI in FS 5.3 and 7.1?
Thank you so much,
best wishes,
Elisabetta



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Re: [Freesurfer] LGI FS 7.1

2021-07-09 Thread Douglas N. Greve


I'm not sure what you mean. Can you elaborate?

On 6/30/2021 5:05 PM, Del Re, Elisabetta wrote:


External Email - Use Caution

External Email - Use Caution

Thank you so much.
I am still in doubt as to whether adjust/normalize for brain volume or 
otherwise surface area before comparing groups.

Thank you for your advise,
best wishes,
Elisabetta

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Sunday, June 20, 2021 10:34 AM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] LGI FS 7.1
The biggest changes are intensity normalization and highres support, 
but many more changes. See the release notes
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes 
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On 6/9/2021 10:17 AM, Del Re, Elisabetta wrote:


External Email - Use Caution

External Email - Use Caution


Dear FS team,
what are differences if any between LGI in FS 5.3 and 7.1?
Thank you so much,
best wishes,
Elisabetta

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Re: [Freesurfer] LGI FS 7.1

2021-06-30 Thread Del Re, Elisabetta

External Email - Use Caution

Thank you so much.
I am still in doubt as to whether adjust/normalize for brain volume or 
otherwise surface area before comparing groups.
Thank you for your advise,
best wishes,
Elisabetta

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Sunday, June 20, 2021 10:34 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] LGI FS 7.1

The biggest changes are intensity normalization and highres support, but many 
more changes. See the release notes
https://secure-web.cisco.com/1xB0JoEP4-fG6EBFVYpZNgm_wWEEh-A2gLPM-xdJP5exIJKbf7w6aDNPwqYmKJIR8SrNy1xr6DJo9iYqEnbwjCYfUyZQRlY8Hd4MU-d6yggFqQmT66AdhaeuTQeUQ7AkgibL7x5UqcEljyQL1RT0KBiyOnReezLP4Z8--PU2iDuGic9cXeEnro0Xpv-Tzp6NbIfk6obBLB7iAzGhkhUqZQGiUVwZGVeRjVT6zSrZjqVvuMa21nIKQ6S9MLRSvddGz9Fo4YxwtSgSSaqFZhiC6qQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes


On 6/9/2021 10:17 AM, Del Re, Elisabetta wrote:

External Email - Use Caution

External Email - Use Caution

Dear FS team,
what are differences if any between LGI in FS 5.3 and 7.1?
Thank you so much,
best wishes,
Elisabetta



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Re: [Freesurfer] LGI FS 7.1

2021-06-20 Thread Douglas N. Greve

The biggest changes are intensity normalization and highres support, but 
many more changes. See the release notes

https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes


On 6/9/2021 10:17 AM, Del Re, Elisabetta wrote:


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Dear FS team,
what are differences if any between LGI in FS 5.3 and 7.1?
Thank you so much,
best wishes,
Elisabetta

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[Freesurfer] LGI FS 7.1

2021-06-09 Thread Del Re, Elisabetta

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Dear FS team,
what are differences if any between LGI in FS 5.3 and 7.1?
Thank you so much,
best wishes,
Elisabetta
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Re: [Freesurfer] LGI error on FS7.1

2021-05-11 Thread Douglas N. Greve

This was fixed in 7.11. You can use that version or copy the attached 
file to this location

$FREESURFER_HOME/matlab/freesurfer_read_surf.m

On 5/11/2021 2:28 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:

Hi,

I am using Matlab R2014a, and FS7.1.0

and receiving this error when I try to run -localGI. Is there a 
package I might be missing? Or am I using an outdated version of Matlab?

=
mris_smooth -nw -n 30 
/mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main 
./lh.pial-outer-smoothed

=
smoothing for 30 iterations
smoothing surface tessellation for 30 iterations...
smoothing complete - recomputing first and second fundamental forms...
=
mris_euler_number ./lh.pial-outer-smoothed
=
euler # = v-e+f = 2g-2: 61554 - 184656 + 123104 = 2 --> 0 holes
  F =2V-4:  123104 = 123108-4 (0)
  2E=3F:    369312 = 369312 (0)

total defect index = 0
=
mris_convert -n lh.pial-outer-smoothed 
/mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc

=
=
find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_30700_.m'); 
exit

=

    < M A T L A B (R) >
  Copyright 1984-2014 The MathWorks, Inc.
    R2014a (8.3.0.532) 64-bit (glnxa64)
 February 11, 2014
.

.

.

To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.

>> Warning: Input argument must be a string.
> In ver at 41
  In freesurfer_read_surf at 70
  In find_corresponding_center_FSformat at 26
Error using fprintf
Function is not defined for 'struct' inputs.

Error in freesurfer_read_surf (line 70)
fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

Error in find_corresponding_center_FSformat (line 26)
[mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);

>>
ERROR: find_corresponding_center_FSformat did not complete successfully!
Command exited with non-zero status 1
@#@FSTIME  2021:05:11:17:18:12 mris_compute_lgi N 2 e 31.58 S 6.20 U 
53.23 P 188% M 1319608 F 0 R 1468406 W 0 c 71733 w 7023 I 8832 O 30496 
L 17.98 17.99 18.00

@#@FSLOADPOST 2021:05:11:17:18:44 mris_compute_lgi N 2 17.35 17.83 17.95
Linux Gamma 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2+deb8u3 
(2016-07-02) x86_64 GNU/Linux

recon-all -s 24015_S5437DFD_ASSET exited with ERRORS at Tue May 11 
17:18:44 EDT 2021

For more details, see the log file 
/mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/scripts/recon-all.log
To report a problem, see 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--

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function [vertices, faces] = freesurfer_read_surf(fname)

% freesurfer_read_surf - FreeSurfer I/O function to read a surface file
% 
% [vertices, faces] = freesurfer_read_surf(fname)
% 
% Reads the vertex coordinates (mm) and face lists from a surface file.
% 
% Surface files are stored as either triangulations or quadrangulations.
% That is, for a triangulation, each face is defined by 3 vertices.  For a
% quadrangulation, each face is defined by 4 vertices.  The rows of 'faces'
% contain indices into the rows of 'vertices', the latter holds the XYZ
% coordinates of each vertex.
%
% The freesurfer faces index the vertices in counter-clockwise order (when
% viewed from the outside of the surface).  This is consistent with a
% right-hand rule.  If we have vertices
%
% C   B
%
%
%   A
%
% Then we can calculate an edge vector from A to B (ie, AB = B - A) and
% another edge vector from A to C (ie, AC = C - A).  If you form a "gun"
% with your thumb and forefinger of the right hand, then align your thumb
% with the AB vector and your forefinger with the AC vector, your palm is
% facing out of the screen and extending your middle finger in the
% orthogonal direction to the plane of the screen will give the outward
% surface normal of the triangle ABC.

[Freesurfer] LGI error on FS7.1

2021-05-11 Thread Zeng, Victor (BIDMC - Keshavan - Psychiatry)

Hi,


I am using Matlab R2014a, and FS7.1.0


and receiving this error when I try to run -localGI. Is there a package I might 
be missing? Or am I using an outdated version of Matlab?


=
mris_smooth -nw -n 30 
/mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main
 ./lh.pial-outer-smoothed
=
smoothing for 30 iterations
smoothing surface tessellation for 30 iterations...
smoothing complete - recomputing first and second fundamental forms...
=
mris_euler_number ./lh.pial-outer-smoothed
=
euler # = v-e+f = 2g-2: 61554 - 184656 + 123104 = 2 --> 0 holes
  F =2V-4:  123104 = 123108-4 (0)
  2E=3F:369312 = 369312 (0)

total defect index = 0
=
mris_convert -n lh.pial-outer-smoothed 
/mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc
=
=
find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_30700_.m');
 exit
=

< M A T L A B (R) >
  Copyright 1984-2014 The MathWorks, Inc.
R2014a (8.3.0.532) 64-bit (glnxa64)
 February 11, 2014
.

.

.

To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit 
http://secure-web.cisco.com/19tcoYq0b9VO4ndLxRqJ8z0rI8AoZ3PjjUlX3NMoW1hFDf9ttZf6sacIdCRKlGFtZmegJWn70rcpkiwHSkFXvvbQOHH177lUt_yW-pC9sSqpOioPl75kS4whrNmvis7o2T33ZU5Gv0WbTPhvV7Io8oSJ6trWPIbAw6pNHbZO7BOe_5BzQ9rBX4PCemrDYBA7lrmjStJB4tithcTY6M7UpKz21q5HvSWus7YdzRnacG5y3y_b6MdREEqwYThfXN3Oj2o1HC9-miVTQpE7AjxNNyw/http%3A%2F%2Fwww.mathworks.com.

>> Warning: Input argument must be a string.
> In ver at 41
  In freesurfer_read_surf at 70
  In find_corresponding_center_FSformat at 26
Error using fprintf
Function is not defined for 'struct' inputs.

Error in freesurfer_read_surf (line 70)
fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

Error in find_corresponding_center_FSformat (line 26)
[mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);

>>
ERROR: find_corresponding_center_FSformat did not complete successfully!
Command exited with non-zero status 1
@#@FSTIME  2021:05:11:17:18:12 mris_compute_lgi N 2 e 31.58 S 6.20 U 53.23 P 
188% M 1319608 F 0 R 1468406 W 0 c 71733 w 7023 I 8832 O 30496 L 17.98 17.99 
18.00
@#@FSLOADPOST 2021:05:11:17:18:44 mris_compute_lgi N 2 17.35 17.83 17.95
Linux Gamma 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2+deb8u3 (2016-07-02) 
x86_64 GNU/Linux

recon-all -s 24015_S5437DFD_ASSET exited with ERRORS at Tue May 11 17:18:44 EDT 
2021

For more details, see the log file 
/mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/scripts/recon-all.log
To report a problem, see 
http://secure-web.cisco.com/1tb0Ac8lCR6JdEw2vyP10SJNFvPDfcz-cQZjb7S8SDNovcHCASZ0ejX-iVoBNkur1EemshwyuuYVhC1g2gQDPTOlKTLP_pUKrzO7iFGxZfxieeZkSMxV2Re8Simd716uBVxefYTUs5w5s0UeeaqZRMQ_XTeSeG9OoigTxYckc3jS3NhIsMo10zR55S4l_Hor3dLwqvoJ8bkFjNt7alnwyI1ZSKuy6r6-iNb8eTD--RhD_GkzvNdsXCms8klaaNBbRvRKG56tTdIxa_tmotWtHaw/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting



Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--



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Re: [Freesurfer] LGI quality control {Disarmed}

2020-11-05 Thread Douglas N. Greve

When you click on the gray areas, is the value 0 or just something very 
close to 0? You may need to set the lower threshold (default is 2). 
Also, I would recommend using freeview via tksurferfv (same command line 
as tksurfer)


On 11/4/2020 2:12 PM, Nelson, Eric wrote:


External Email - Use Caution

Hello,

I am using FreeSurfer 7.1.1 to run LGI and have done so successfully. 
I am now trying to quality check my data using tksurfer as described 
on the wiki


/tksurfer my_subject_id lh inflated -overlay lh.pial_lgi/

However the LGI overlay is not covering the entirety of the inflated 
brain. Specifically the medial frontal surface and some subcortical 
are not measured for LGI.  Here is a link of the overlay images for a 
few subjects: *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://www.dropbox.com/s/9pt8rti4yjudrza/LGI_QC.png?dl=0. I 
. 
I haven’t been able to find any images of what this overlay should 
look like so I don’t know if this is expected or if something has gone 
wrong with the processing. Any feedback would be greatly appreciated


Best,

Eric


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[Freesurfer] LGI quality control {Disarmed}

2020-11-04 Thread Nelson, Eric

External Email - Use Caution

Hello,

I am using FreeSurfer 7.1.1 to run LGI and have done so successfully. I am now 
trying to quality check my data using tksurfer as described on the wiki
tksurfer my_subject_id lh inflated -overlay lh.pial_lgi
However the LGI overlay is not covering the entirety of the inflated brain. 
Specifically the medial frontal surface and some subcortical are not measured 
for LGI.  Here is a link of the overlay images for a few subjects: 
https://secure-web.cisco.com/1FvGKanOWU0exqsmfZZWyCdCgTFgqf8kB2BXdsF-5A035k1rc5i2ECL9Bt-sn8Wd9sg8LgyvKPIHD_K3n3d8aIlOYT7vHfQVCA6sCq1NlzFrs_Vjn74CGIhg1nIjX_csnDAnz8kzCUBLMiTd7c6DTZvaQ5aM3UeKBq-PVh8O5XAwOUvbQ3_05ie7fb0YGRsg8Q2DrGwEWtgQCqpUnhvIPdA/https%3A%2F%2Fwww.dropbox.com%2Fs%2F9pt8rti4yjudrza%2FLGI_QC.png%3Fdl%3D0.
 
I.
 I haven't been able to find any images of what this overlay should look like 
so I don't know if this is expected or if something has gone wrong with the 
processing. Any feedback would be greatly appreciated

Best,

Eric

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Re: [Freesurfer] LGI output question

2020-10-27 Thread Douglas N. Greve

I'm not sure what you mean by the mean area for the different LGI 
values. Can you elaborate?


On 10/20/2020 6:46 PM, Lab of Autism and Developmental Neuroscience, Lab 
of Autism and Developmental Neuroscience wrote:


External Email - Use Caution

Dear Freesurfer experts,

I have performed LGI for one of my subject pools and I was wondering 
if I can compute the mean area for the different LGI values instead of 
the area in the output tables? How should I edit the code below to 
accomplish this? Thank you and stay safe!
mri_segstats --annot my_subject_id lh aparc --i 
$SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats


All the best,
Alex

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[Freesurfer] LGI output question

2020-10-20 Thread Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience

External Email - Use Caution

Dear Freesurfer experts,

I have performed LGI for one of my subject pools and I was wondering if I
can compute the mean area for the different LGI values instead of the area
in the output tables? How should I edit the code below to accomplish this?
Thank you and stay safe!
mri_segstats --annot my_subject_id lh aparc --i
$SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats

All the best,
Alex
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Re: [Freesurfer] LGI value extraction

2020-09-29 Thread Douglas N. Greve

That is really LGI. aparcstats2table just defaults to "thickness". But 
you should double check that the value you see in


lh.aparc_lgi.stats is the same as in result_lgi_lh.txt

On 9/29/2020 12:38 PM, 祝菲 wrote:


External Email - Use Caution

Dear expert,

I have used freesurfer v6.0 to calculate local Gyrification index ( 
LGI ). And  I have output the file named lh.pial_lgi and extracted the 
value of LGI by using the following command:


> mris_anatomical_stats -a ${SUBJECTS_DIR}/S005/label/lh.aparc.annot -t 
pial_lgi -f ${SUBJECTS_DIR}/S005/stats/lh.aparc_lgi.stats S005 lh
> aparcstats2table --subjects S005 --hemi lh --meas thickness --skip 
—parc aparc_lgi --tablefile result_lgi_lh.txt
  However, I found that the header of the output result showed the 
“thickness" instead of “LGI". Does this “thickness" represent the 
index of “LGI"? I have attached the result of one sample  in the 
attachment. Thank you again for taking your precious time to solve my 
problem！



kind regards


zhu fei


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[Freesurfer] LGI value extraction

2020-09-29 Thread 祝菲

External Email - Use CautionDear expert,I have used freesurfer v6.0 to calculate local Gyrification index ( LGI ). And  I have output the file named lh.pial_lgi and extracted the value of LGI by using the following command:> mris_anatomical_stats -a ${SUBJECTS_DIR}/S005/label/lh.aparc.annot -t pial_lgi -f ${SUBJECTS_DIR}/S005/stats/lh.aparc_lgi.stats S005 lh
> aparcstats2table --subjects S005 --hemi lh --meas thickness --skip —parc aparc_lgi --tablefile  result_lgi_lh.txt	  However, I found that the header of the output result showed the “thickness" instead of “LGI". Does this “thickness" represent the index of “LGI"? I have attached the result of one sample  in the attachment. Thank you again for taking your precious time to solve my problem！lh.aparc_lgi.thickness  lh_bankssts_thickness   
lh_caudalanteriorcingulate_thicknesslh_caudalmiddlefrontal_thickness
lh_cuneus_thickness lh_entorhinal_thickness lh_fusiform_thickness   
lh_inferiorparietal_thickness   lh_inferiortemporal_thickness   
lh_isthmuscingulate_thickness   lh_lateraloccipital_thickness   
lh_lateralorbitofrontal_thickness   lh_lingual_thickness
lh_medialorbitofrontal_thicknesslh_middletemporal_thickness 
lh_parahippocampal_thicknesslh_paracentral_thickness
lh_parsopercularis_thicknesslh_parsorbitalis_thickness  
lh_parstriangularis_thickness   lh_pericalcarine_thickness  
lh_postcentral_thicknesslh_posteriorcingulate_thickness 
lh_precentral_thickness lh_precuneus_thickness  
lh_rostralanteriorcingulate_thickness   lh_rostralmiddlefrontal_thickness   
lh_superiorfrontal_thicknesslh_superiorparietal_thickness   
lh_superiortemporal_thickness   lh_supramarginal_thickness  
lh_frontalpole_thicknesslh_temporalpole_thickness   
lh_transversetemporal_thickness lh_insula_thickness BrainSegVolNotVent  
eTIV
S0053.692   1.994   3.605   3.123   2.763   3.005   3.569   3.008   3.253   
2.918   2.821   3.076   2.218   3.594   3.046   2.474   4.456   3.268   3.812   
3.058   3.765   2.548   3.798   3.094   2.166   3.125   2.342   3.185   4.308   
3.814   2.103   2.762   4.964.501   1254238.0   1695575.52621
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Re: [Freesurfer] lGI permutation and monte-carlo

2020-06-12 Thread Douglas N. Greve




On 6/9/2020 11:27 AM, Avi Gharehgazlou wrote:


External Email - Use Caution

Thank you so much for your input, it was very helpful and I 
really appreciate it.


Regarding your question with relation to my 4th question, when I run 
the below command line to visualize my results after correcting for 
multiple comparisons using monte-carlo at 1.3 significance level in 
this example, I assumed the clusters that appear on freeview are only 
my significant clusters (clusters that survived monte carlo 
correction) since I put " cache.th13.abs.sig.cluster.mgh" and then as 
overlay " cache.th13.abs.sig.ocn.annot " in my command line. If not, 
will you please tell me how I can see only clusters that are 
significant after correction for multiple comparisons (at 1.3 sig 
level in this case)?

Your interpretation is correct.


Also, in my command line, I can put either lh.pial or lh.inflated to 
see the results//clusters on the pial or inflated surface, 
respectively. Correct?

Correct


vglrun freeview 
-f $SUBJECTS_DIR/fsaverage/surf/lh.pial:overlay=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.cluster.mgh:overlay_threshold=1.3,5:annot=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.ocn.annot -viewport 
3d


Thank you so much,

Avi



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Re: [Freesurfer] lGI permutation and monte-carlo

2020-06-09 Thread Avi Gharehgazlou

External Email - Use Caution

Thank you so much for your input, it was very helpful and I
really appreciate it.

Regarding your question with relation to my 4th question, when I run the
below command line to visualize my results after correcting for multiple
comparisons using monte-carlo at 1.3 significance level in this example, I
assumed the clusters that appear on freeview are only my significant
clusters (clusters that survived monte carlo correction) since I put "
cache.th13.abs.sig.cluster.mgh" and then as overlay "
cache.th13.abs.sig.ocn.annot " in my command line. If not, will you please
tell me how I can see only clusters that are significant after correction
for multiple comparisons (at 1.3 sig level in this case)?

Also, in my command line, I can put either lh.pial or lh.inflated to see
the results//clusters on the pial or inflated surface, respectively.
Correct?

vglrun freeview
-f 
$SUBJECTS_DIR/fsaverage/surf/lh.pial:overlay=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.cluster.mgh:overlay_threshold=1.3,5:annot=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.ocn.annot
-viewport
3d

Thank you so much,

Avi
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Re: [Freesurfer] lGI permutation and monte-carlo

2020-06-09 Thread Douglas N. Greve

On 6/8/2020 8:12 PM, Avi Gharehgazlou wrote:

External Email - Use Caution

Hi experts,

Upon reading your 2018 paper (cited below) and following threads on
the archives, I am aware that I should use permutation testing for lGI
analyses rather than monte carlo at p<0.05. However, I have a few
questions below that I would really appreciate your input on:

1. For permutation testing on lGI data, what are the CFT and cwp
levels you recommend? Would it be appropriate for me to use CFT=1.3
and cwp=0.05?
cwp=0.05 is always appropriate. The CFT is somewhat arbitrary. For
parametric methods, a high CFT is necessary; this often becomes a
problem because, if you set the CFT too high, you will not have any
voxels left. But for permutation, you can really set it to anything you
want.

2. Will you confirm my interpretation for permutation command line below?
mri_glmfit-sim --glmdir lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir --perm
1000 2 abs --perm-resid --cwp 0.05 --2spaces --bg 1

Above command indicates that I used a cluster-forming threshold of
p<0.01 and a cluster-wise significance threshold of p<0.05 - meaning
that clusters are initially obtained using p<0.01 (CFT) but I report
them in my paper if they meet additional cluster-wise probability of
p<0.05 (cwp). Both are two-tailed (since I am using abs). Is this
interpretation correct?

Yes

3. Would it be okay to correct with monte carlo using CFT=3 and cwp=
0.05 (below command line) instead of permutation testing for lGI data?
mri_glmfit-sim --glmdir lh.ASDvsADHD.glmdir --cache 3 abs --cwp 0.05
--2spaces
I don't know. CFT=3 was mostly acceptable for thickenss, area, and
volume, but I imagine that lGI would be worse than any of those.

3. I am not smoothing my lGI data (as lGI is a relatively smooth
measure and to keep this consistent with the literature I have
reviewed), however, after reading your 2018 paper, I wanted to ask if
this is appropriate? Your paper recommends CFT<0.001 and FWHM>10mm for
surface area analyses. Do I have to smooth lGI when doing a)
permutation testing or b) monte carlo correction (steps 1 and 3
above)? If yes, what level of smoothness do you recommend?
I don't know without doing the study. lGI is already has a lot of
smoothness in it by the way it is created. The real question is how
heavy the smoothness tails are; I suspect pretty heavy.

4. After correcting with monte-carlo at p<0.05 - When I use the below
command line to see my corrected results in freeview, I notice the
significant cluster is gray rather than blue (I know it should be blue
because I've ran this same analysis using QDEC). In order to see this
cluster's true colour (and thus be able to interpret my results) do I
have to change the threshold by clicking ‘show outline overlay’ then
clicking ‘configure’ and setting the min value to 1.3? Is this the
correct way of visualizing my corrected results?

vglrun freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.pial:overlay=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.cluster.mgh:overlay_threshold=1.3,5:annot=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.ocn.annot
-viewport 3d
It looks like you already have the min value at 1.3, which should be
sufficient. How do you know that your cluster is significant?

reference
Greve DN & Fischl B. 2018. False positive rates in surface-based
anatomical analysis. NeuroImage.

Thank you so much,

Avi

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[Freesurfer] lGI permutation and monte-carlo

2020-06-08 Thread Avi Gharehgazlou

External Email - Use Caution

Hi experts,

Upon reading your 2018 paper (cited below) and following threads on the
archives, I am aware that I should use permutation testing for lGI analyses
rather than monte carlo at p<0.05. However, I have a few questions below
that I would really appreciate your input on:

1. For permutation testing on lGI data, what are the CFT and cwp levels you
recommend? Would it be appropriate for me to use CFT=1.3 and cwp=0.05?

2. Will you confirm my interpretation for permutation command line below?
mri_glmfit-sim --glmdir lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir --perm 1000 2
abs --perm-resid --cwp 0.05 --2spaces --bg 1

Above command indicates that I used a cluster-forming threshold of p<0.01
and a cluster-wise significance threshold of p<0.05 - meaning that clusters
are initially obtained using p<0.01 (CFT) but I report them in my paper if
they meet additional cluster-wise probability of p<0.05 (cwp). Both are
two-tailed (since I am using abs). Is this interpretation correct?

3. I am not smoothing my lGI data (as lGI is a relatively smooth measure
and to keep this consistent with the literature I have reviewed), however,
after reading your 2018 paper, I wanted to ask if this is appropriate? Your
paper recommends CFT<0.001 and FWHM>10mm for surface area analyses. Do I
have to smooth lGI when doing a) permutation testing or b) monte carlo
correction (steps 1 and 3 above)? If yes, what level of smoothness do you
recommend?

4. After correcting with monte-carlo at p<0.05 - When I use the below
command line to see my corrected results in freeview, I notice the
significant cluster is gray rather than blue (I know it should be blue
because I've ran this same analysis using QDEC). In order to see this
cluster's true colour (and thus be able to interpret my results) do I have
to change the threshold by clicking ‘show outline overlay’ then clicking
‘configure’ and setting the min value to 1.3? Is this the correct way of
visualizing my corrected results?

reference
Greve DN & Fischl B. 2018. False positive rates in surface-based anatomical
analysis. NeuroImage.

Thank you so much,

Avi
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[Freesurfer] LGI and Global GI

2020-05-27 Thread Alexopoulos, Dimitrios

External Email - Use Caution

HI,

I have generated the LGI for a group of pediatric subjects. Is there a way to 
compute a single Global gyrification index measure  for each subject?

Jim,



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Re: [Freesurfer] LGI problem

2020-05-22 Thread Angela Favaro

External Email - Use Caution

Hi Doug, 
I had the identical problem (failure at segmentation stage, as described below) 
in 4 subjects of my dataset. I have no possibility to run analyses on a linux 
machine…
Since all 4 subjects had no problem using Freesurfer 6, is it so wrong to use 
freesurfer 6 only for these 4 subjects?
Or have you any other suggestions?

Thank you for any help

Angela




> Il giorno 15 mag 2020, alle ore 23:26, Angela Favaro  
> ha scritto:
> 
> External Email - Use Caution
> 
> 
> Hi doug, 
> I tried to re-run 3 or 4 times and always failed at the segmentation stage…
> I have no linux machine, but I can try in a mac computer with a different 
> OS...
> thank you!
> 
> Angela
> 
> 
>> Il giorno 15 mag 2020, alle ore 23:08, Douglas N. Greve 
>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>> 
>> Hi Angela, I cannot replicate this error. If you re-run, does it always exit 
>> with error? You can try this quickly be running
>> 
>> setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/Aachen
>> cd /Users/angelafavaro/Desktop/Aachen/subj220/mri
>> mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta 
>> /Users/angelafavaro/Desktop/Aachen/subj220/mri/transforms/cc_up.lta subj220
>> 
>> One factor may be that I'm using CentOS and not Mac. Do you have a linux 
>> machine you can try it on?
>> 
>> 
>> 
>> On 5/15/2020 10:59 AM, Angela Favaro wrote:
>>> External Email - Use Caution
>>> 
>>> I have uploaded to you the data using the Martinos Center FileDrop
>>> Hope is a good option for you
>>> 
>>> Thank you
>>> Angela
>>> 
 Il giorno 15 mag 2020, alle ore 16:40, Angela Favaro 
 mailto:angela.fav...@unipd.it>> ha scritto:
 
 External Email - Use Caution
 
 
 Hi Doug, 
 I have some problem in uploading my subj.tar.gz using ftp. I am using a 
 MacOs Catalina and, although I am able to connect to the FTP site and open 
 the incoming window (also in binary mode), commands are not working...
 
 I am trying to overcome the problem.
 Is there any other method to transfer the data set?
 Thank you
 
 Angela
 
> Il giorno 15 mag 2020, alle ore 00:15, Douglas N. Greve 
> mailto:dgr...@mgh.harvard.edu>> ha scritto:
> 
> Hmmm, I don't know. Can you upload the data set? Follow these instructions
> 
> From the linux command line,
> Create the file you want to upload, eg, 
> cd $SUBJECTS_DIR
> tar cvfz subject.tar.gz ./subject
> Now log  into our anonymous FTP site:
> ftp surfer.nmr.mgh.harvard.edu 
> It will ask you for a user name: use "anonymous" (no quotes)
> It will ask you for a password: use "anonymous" (no quotes)
> cd transfer/incoming
> binary
> put subject.tar.gz
> Send an email that the file has been and the name of the file.
> 
> 
> On 5/14/2020 5:03 PM, Angela Favaro wrote:
>> External Email - Use Caution
>> 
>> Thank you Doug!
>> It works! Great!
>> 
>> 
>> I have another problem: I am reprocessing all my database with 
>> freesurfer 7.1.0, but in one subject segmentation failed.
>> I had no problem with this subjects using freesurfer 6
>> What can be the problem?
>> 
>> I attach the log
>> 
>> Thank you for any help!
>> 
>> Angela
>> 
>> 
>> 
>>> Il giorno 14 mag 2020, alle ore 17:06, Douglas N. Greve 
>>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>>> 
>>> 
>>> Someone just pointed out that I posted the wrong file. Here is the 
>>> correct one. Copy it to the same folder
>>> 
>>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m 
>>> 
>>> 
>>> 
>>> On 5/13/2020 11:01 PM, Douglas N. Greve wrote:
 
 Download this file
 https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m
  
 
 and copy it into $FREESURFER_HOME/matlab
 and rerun. Let me know if that fixes it.
 
 
 
 On 5/13/2020 5:57 PM, Angela Favaro wrote:
> External Email - Use Caution
> 
> Please find attached the log
> Thank you
> Angela
> 
> 
> 
>> Il giorno 13 mag 2020, alle ore 23:35, Douglas N. Greve 
>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>> 
>> Are you running this from recon-all? If so send the recon-all.log. 
>> If from the command line, send the command-line and all terminal 
>> output
>> 
>> On 5/13/2020 5:28 PM, Angela Favaro wrote:
>>> External Email - Use Caution
>>>

Re: [Freesurfer] LGI problem

2020-05-15 Thread Angela Favaro

External Email - Use Caution

Hi doug, 
I tried to re-run 3 or 4 times and always failed at the segmentation stage…
I have no linux machine, but I can try in a mac computer with a different OS...
thank you!

Angela


> Il giorno 15 mag 2020, alle ore 23:08, Douglas N. Greve 
>  ha scritto:
> 
> Hi Angela, I cannot replicate this error. If you re-run, does it always exit 
> with error? You can try this quickly be running
> 
> setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/Aachen
> cd /Users/angelafavaro/Desktop/Aachen/subj220/mri
> mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta 
> /Users/angelafavaro/Desktop/Aachen/subj220/mri/transforms/cc_up.lta subj220
> 
> One factor may be that I'm using CentOS and not Mac. Do you have a linux 
> machine you can try it on?
> 
> 
> 
> On 5/15/2020 10:59 AM, Angela Favaro wrote:
>> External Email - Use Caution
>> 
>> I have uploaded to you the data using the Martinos Center FileDrop
>> Hope is a good option for you
>> 
>> Thank you
>> Angela
>> 
>>> Il giorno 15 mag 2020, alle ore 16:40, Angela Favaro 
>>> mailto:angela.fav...@unipd.it>> ha scritto:
>>> 
>>> External Email - Use Caution
>>> 
>>> 
>>> Hi Doug, 
>>> I have some problem in uploading my subj.tar.gz using ftp. I am using a 
>>> MacOs Catalina and, although I am able to connect to the FTP site and open 
>>> the incoming window (also in binary mode), commands are not working...
>>> 
>>> I am trying to overcome the problem.
>>> Is there any other method to transfer the data set?
>>> Thank you
>>> 
>>> Angela
>>> 
 Il giorno 15 mag 2020, alle ore 00:15, Douglas N. Greve 
 mailto:dgr...@mgh.harvard.edu>> ha scritto:
 
 Hmmm, I don't know. Can you upload the data set? Follow these instructions
 
 From the linux command line,
 Create the file you want to upload, eg, 
 cd $SUBJECTS_DIR
 tar cvfz subject.tar.gz ./subject
 Now log  into our anonymous FTP site:
 ftp surfer.nmr.mgh.harvard.edu 
 It will ask you for a user name: use "anonymous" (no quotes)
 It will ask you for a password: use "anonymous" (no quotes)
 cd transfer/incoming
 binary
 put subject.tar.gz
 Send an email that the file has been and the name of the file.
 
 
 On 5/14/2020 5:03 PM, Angela Favaro wrote:
> External Email - Use Caution
> 
> Thank you Doug!
> It works! Great!
> 
> 
> I have another problem: I am reprocessing all my database with freesurfer 
> 7.1.0, but in one subject segmentation failed.
> I had no problem with this subjects using freesurfer 6
> What can be the problem?
> 
> I attach the log
> 
> Thank you for any help!
> 
> Angela
> 
> 
> 
>> Il giorno 14 mag 2020, alle ore 17:06, Douglas N. Greve 
>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>> 
>> 
>> Someone just pointed out that I posted the wrong file. Here is the 
>> correct one. Copy it to the same folder
>> 
>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m 
>> 
>> 
>> 
>> On 5/13/2020 11:01 PM, Douglas N. Greve wrote:
>>> 
>>> Download this file
>>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m
>>>  
>>> 
>>> and copy it into $FREESURFER_HOME/matlab
>>> and rerun. Let me know if that fixes it.
>>> 
>>> 
>>> 
>>> On 5/13/2020 5:57 PM, Angela Favaro wrote:
 External Email - Use Caution
 
 Please find attached the log
 Thank you
 Angela
 
 
 
> Il giorno 13 mag 2020, alle ore 23:35, Douglas N. Greve 
> mailto:dgr...@mgh.harvard.edu>> ha scritto:
> 
> Are you running this from recon-all? If so send the recon-all.log. If 
> from the command line, send the command-line and all terminal output
> 
> On 5/13/2020 5:28 PM, Angela Favaro wrote:
>> External Email - Use Caution
>> 
>> Hi Doug!
>> yes, it run under version 6!
>> Please let me know if it is something that can be solved
>> Thank you
>> Angela
>> 
>> 
>>> Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve 
>>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>>> 
>>> Does it run under version 6? We are not really supporting lGI 
>>> anymore, but maybe we can get it to work
>>> 
>>> On 5/13/2020 4:24 PM, Angela Favaro wrote:
 External Email - Use Caution
 
 
 Hi all, 
 I am using the new version of

Re: [Freesurfer] LGI problem

2020-05-15 Thread Douglas N. Greve

Hi Angela, I cannot replicate this error. If you re-run, does it always 
exit with error? You can try this quickly be running

setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/Aachen
cd /Users/angelafavaro/Desktop/Aachen/subj220/mri
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta 
/Users/angelafavaro/Desktop/Aachen/subj220/mri/transforms/cc_up.lta subj220

One factor may be that I'm using CentOS and not Mac. Do you have a linux 
machine you can try it on?

On 5/15/2020 10:59 AM, Angela Favaro wrote:

External Email - Use Caution

I have uploaded to you the data using the Martinos Center FileDrop
Hope is a good option for you

Thank you
Angela

Il giorno 15 mag 2020, alle ore 16:40, Angela Favaro 
mailto:angela.fav...@unipd.it>> ha scritto:

External Email - Use Caution

Hi Doug,
I have some problem in uploading my subj.tar.gz using ftp. I am using 
a MacOs Catalina and, although I am able to connect to the FTP site 
and open the incoming window (also in binary mode), commands are not 
working...

I am trying to overcome the problem.
Is there any other method to transfer the data set?
Thank you

Angela

Il giorno 15 mag 2020, alle ore 00:15, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

Hmmm, I don't know. Can you upload the data set? Follow these 
instructions

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu 
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.

On 5/14/2020 5:03 PM, Angela Favaro wrote:

External Email - Use Caution

Thank you Doug!
It works! Great!

I have another problem: I am reprocessing all my database with 
freesurfer 7.1.0, but in one subject segmentation failed.

I had no problem with this subjects using freesurfer 6
What can be the problem?

I attach the log

Thank you for any help!

Angela

Il giorno 14 mag 2020, alle ore 17:06, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

Someone just pointed out that I posted the wrong file. Here is the 
correct one. Copy it to the same folder

https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m

On 5/13/2020 11:01 PM, Douglas N. Greve wrote:

Download this file
https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m
and copy it into $FREESURFER_HOME/matlab
and rerun. Let me know if that fixes it.

On 5/13/2020 5:57 PM, Angela Favaro wrote:

External Email - Use Caution

Please find attached the log
Thank you
Angela

Il giorno 13 mag 2020, alle ore 23:35, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha 
scritto:

Are you running this from recon-all? If so send the 
recon-all.log. If from the command line, send the command-line 
and all terminal output

On 5/13/2020 5:28 PM, Angela Favaro wrote:

External Email - Use Caution

Hi Doug!
yes, it run under version 6!
Please let me know if it is something that can be solved
Thank you
Angela

Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha 
scritto:

Does it run under version 6? We are not really supporting lGI 
anymore, but maybe we can get it to work

On 5/13/2020 4:24 PM, Angela Favaro wrote:

External Email - Use Caution

Hi all,
I am using the new version of Freesurfer 7.1.0
And I am finding problems in running gyrification analysis.
I have Matlab 2016a (and 2019b) with the toolbox image 
processing

The error is after the command 
find_corresponding_center_FSformat

Matlab seems to start, but then the following message appears:

>> Warning: Input argument must be a string.
> In ver (line 41)
In freesurfer_read_surf (line 70)
In find_corresponding_center_FSformat (line 26)
Error using fprintf
Function is not defined for 'struct' inputs.

Error in freesurfer_read_surf (line 70)
fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

Error in find_corresponding_center_FSformat (line 26)
[mesh_pial.vertices, mesh_pial.faces] = 
freesurfer_read_surf(pial);

>> 
ERROR: find_corresponding_center_FSformat did not complete 
successfully!

I tried with both the Matlab version, but the error is the same
Any help is appreciated. Thank you so much

Angela

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Re: [Freesurfer] LGI problem

2020-05-15 Thread Angela Favaro

External Email - Use Caution

I have uploaded to you the data using the Martinos Center FileDrop
Hope is a good option for you

Thank you
Angela

> Il giorno 15 mag 2020, alle ore 16:40, Angela Favaro  
> ha scritto:
> 
> External Email - Use Caution
> 
> 
> Hi Doug, 
> I have some problem in uploading my subj.tar.gz using ftp. I am using a MacOs 
> Catalina and, although I am able to connect to the FTP site and open the 
> incoming window (also in binary mode), commands are not working...
> 
> I am trying to overcome the problem.
> Is there any other method to transfer the data set?
> Thank you
> 
> Angela
> 
>> Il giorno 15 mag 2020, alle ore 00:15, Douglas N. Greve 
>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>> 
>> Hmmm, I don't know. Can you upload the data set? Follow these instructions
>> 
>> From the linux command line,
>> Create the file you want to upload, eg, 
>> cd $SUBJECTS_DIR
>> tar cvfz subject.tar.gz ./subject
>> Now log  into our anonymous FTP site:
>> ftp surfer.nmr.mgh.harvard.edu 
>> It will ask you for a user name: use "anonymous" (no quotes)
>> It will ask you for a password: use "anonymous" (no quotes)
>> cd transfer/incoming
>> binary
>> put subject.tar.gz
>> Send an email that the file has been and the name of the file.
>> 
>> 
>> On 5/14/2020 5:03 PM, Angela Favaro wrote:
>>> External Email - Use Caution
>>> 
>>> Thank you Doug!
>>> It works! Great!
>>> 
>>> 
>>> I have another problem: I am reprocessing all my database with freesurfer 
>>> 7.1.0, but in one subject segmentation failed.
>>> I had no problem with this subjects using freesurfer 6
>>> What can be the problem?
>>> 
>>> I attach the log
>>> 
>>> Thank you for any help!
>>> 
>>> Angela
>>> 
>>> 
>>> 
 Il giorno 14 mag 2020, alle ore 17:06, Douglas N. Greve 
 mailto:dgr...@mgh.harvard.edu>> ha scritto:
 
 
 Someone just pointed out that I posted the wrong file. Here is the correct 
 one. Copy it to the same folder
 
 https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m 
 
 
 
 On 5/13/2020 11:01 PM, Douglas N. Greve wrote:
> 
> Download this file
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m
>  
> 
> and copy it into $FREESURFER_HOME/matlab
> and rerun. Let me know if that fixes it.
> 
> 
> 
> On 5/13/2020 5:57 PM, Angela Favaro wrote:
>> External Email - Use Caution
>> 
>> Please find attached the log
>> Thank you
>> Angela
>> 
>> 
>> 
>>> Il giorno 13 mag 2020, alle ore 23:35, Douglas N. Greve 
>>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>>> 
>>> Are you running this from recon-all? If so send the recon-all.log. If 
>>> from the command line, send the command-line and all terminal output
>>> 
>>> On 5/13/2020 5:28 PM, Angela Favaro wrote:
 External Email - Use Caution
 
 Hi Doug!
 yes, it run under version 6!
 Please let me know if it is something that can be solved
 Thank you
 Angela
 
 
> Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve 
> mailto:dgr...@mgh.harvard.edu>> ha scritto:
> 
> Does it run under version 6? We are not really supporting lGI 
> anymore, but maybe we can get it to work
> 
> On 5/13/2020 4:24 PM, Angela Favaro wrote:
>> External Email - Use Caution
>> 
>> 
>> Hi all, 
>> I am using the new version of Freesurfer 7.1.0
>> And I am finding problems in running gyrification analysis.
>> I have Matlab 2016a (and 2019b) with the toolbox image processing
>> 
>> The error is after the command find_corresponding_center_FSformat
>> 
>> Matlab seems to start, but then the following message appears:
>> 
>> >> Warning: Input argument must be a string. 
>> > In ver (line 41)
>>   In freesurfer_read_surf (line 70)
>>   In find_corresponding_center_FSformat (line 26) 
>> Error using fprintf
>> Function is not defined for 'struct' inputs.
>> 
>> Error in freesurfer_read_surf (line 70)
>> fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));
>> 
>> Error in find_corresponding_center_FSformat (line 26)
>> [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);
>>  
>> >> 
>> ERROR: find_corresponding_center_FSformat did not complete 
>> successfully!
>> 
>> I tried with both the Matlab version, but the error is the same
>>

Re: [Freesurfer] LGI problem

2020-05-15 Thread Angela Favaro

External Email - Use Caution

Hi Doug, 
I have some problem in uploading my subj.tar.gz using ftp. I am using a MacOs 
Catalina and, although I am able to connect to the FTP site and open the 
incoming window (also in binary mode), commands are not working...

I am trying to overcome the problem.
Is there any other method to transfer the data set?
Thank you

Angela

> Il giorno 15 mag 2020, alle ore 00:15, Douglas N. Greve 
>  ha scritto:
> 
> Hmmm, I don't know. Can you upload the data set? Follow these instructions
> 
> From the linux command line,
> Create the file you want to upload, eg, 
> cd $SUBJECTS_DIR
> tar cvfz subject.tar.gz ./subject
> Now log  into our anonymous FTP site:
> ftp surfer.nmr.mgh.harvard.edu
> It will ask you for a user name: use "anonymous" (no quotes)
> It will ask you for a password: use "anonymous" (no quotes)
> cd transfer/incoming
> binary
> put subject.tar.gz
> Send an email that the file has been and the name of the file.
> 
> 
> On 5/14/2020 5:03 PM, Angela Favaro wrote:
>> External Email - Use Caution
>> 
>> Thank you Doug!
>> It works! Great!
>> 
>> 
>> I have another problem: I am reprocessing all my database with freesurfer 
>> 7.1.0, but in one subject segmentation failed.
>> I had no problem with this subjects using freesurfer 6
>> What can be the problem?
>> 
>> I attach the log
>> 
>> Thank you for any help!
>> 
>> Angela
>> 
>> 
>> 
>>> Il giorno 14 mag 2020, alle ore 17:06, Douglas N. Greve 
>>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>>> 
>>> 
>>> Someone just pointed out that I posted the wrong file. Here is the correct 
>>> one. Copy it to the same folder
>>> 
>>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m 
>>> 
>>> 
>>> 
>>> On 5/13/2020 11:01 PM, Douglas N. Greve wrote:
 
 Download this file
 https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m
  
 
 and copy it into $FREESURFER_HOME/matlab
 and rerun. Let me know if that fixes it.
 
 
 
 On 5/13/2020 5:57 PM, Angela Favaro wrote:
> External Email - Use Caution
> 
> Please find attached the log
> Thank you
> Angela
> 
> 
> 
>> Il giorno 13 mag 2020, alle ore 23:35, Douglas N. Greve 
>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>> 
>> Are you running this from recon-all? If so send the recon-all.log. If 
>> from the command line, send the command-line and all terminal output
>> 
>> On 5/13/2020 5:28 PM, Angela Favaro wrote:
>>> External Email - Use Caution
>>> 
>>> Hi Doug!
>>> yes, it run under version 6!
>>> Please let me know if it is something that can be solved
>>> Thank you
>>> Angela
>>> 
>>> 
 Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve 
 mailto:dgr...@mgh.harvard.edu>> ha scritto:
 
 Does it run under version 6? We are not really supporting lGI anymore, 
 but maybe we can get it to work
 
 On 5/13/2020 4:24 PM, Angela Favaro wrote:
> External Email - Use Caution
> 
> 
> Hi all, 
> I am using the new version of Freesurfer 7.1.0
> And I am finding problems in running gyrification analysis.
> I have Matlab 2016a (and 2019b) with the toolbox image processing
> 
> The error is after the command find_corresponding_center_FSformat
> 
> Matlab seems to start, but then the following message appears:
> 
> >> Warning: Input argument must be a string. 
> > In ver (line 41)
>   In freesurfer_read_surf (line 70)
>   In find_corresponding_center_FSformat (line 26) 
> Error using fprintf
> Function is not defined for 'struct' inputs.
> 
> Error in freesurfer_read_surf (line 70)
> fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));
> 
> Error in find_corresponding_center_FSformat (line 26)
> [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);
>  
> >> 
> ERROR: find_corresponding_center_FSformat did not complete 
> successfully!
> 
> I tried with both the Matlab version, but the error is the same
> Any help is appreciated. Thank you so much
> 
> Angela
> 
> 
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>> Freesurfer@nmr.mgh.harvard.edu 
>> 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>> 
> 
>

Re: [Freesurfer] LGI problem

2020-05-14 Thread Douglas N. Greve

Hmmm, I don't know. Can you upload the data set? Follow these instructions

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.

On 5/14/2020 5:03 PM, Angela Favaro wrote:

External Email - Use Caution

Thank you Doug!
It works! Great!

I have another problem: I am reprocessing all my database with 
freesurfer 7.1.0, but in one subject segmentation failed.

I had no problem with this subjects using freesurfer 6
What can be the problem?

I attach the log

Thank you for any help!

Angela

Il giorno 14 mag 2020, alle ore 17:06, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

Someone just pointed out that I posted the wrong file. Here is the 
correct one. Copy it to the same folder

https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m

On 5/13/2020 11:01 PM, Douglas N. Greve wrote:

Download this file
https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m
and copy it into $FREESURFER_HOME/matlab
and rerun. Let me know if that fixes it.

On 5/13/2020 5:57 PM, Angela Favaro wrote:

External Email - Use Caution

Please find attached the log
Thank you
Angela

Il giorno 13 mag 2020, alle ore 23:35, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

Are you running this from recon-all? If so send the recon-all.log. 
If from the command line, send the command-line and all terminal 
output

On 5/13/2020 5:28 PM, Angela Favaro wrote:

External Email - Use Caution

Hi Doug!
yes, it run under version 6!
Please let me know if it is something that can be solved
Thank you
Angela

Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

Does it run under version 6? We are not really supporting lGI 
anymore, but maybe we can get it to work

On 5/13/2020 4:24 PM, Angela Favaro wrote:

External Email - Use Caution

Hi all,
I am using the new version of Freesurfer 7.1.0
And I am finding problems in running gyrification analysis.
I have Matlab 2016a (and 2019b) with the toolbox image processing

The error is after the command find_corresponding_center_FSformat

Matlab seems to start, but then the following message appears:

>> Warning: Input argument must be a string.
> In ver (line 41)
In freesurfer_read_surf (line 70)
In find_corresponding_center_FSformat (line 26)
Error using fprintf
Function is not defined for 'struct' inputs.

Error in freesurfer_read_surf (line 70)
fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

Error in find_corresponding_center_FSformat (line 26)
[mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);

>> 
ERROR: find_corresponding_center_FSformat did not complete 
successfully!

I tried with both the Matlab version, but the error is the same
Any help is appreciated. Thank you so much

Angela

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Re: [Freesurfer] LGI problem

2020-05-14 Thread Douglas N. Greve

Someone just pointed out that I posted the wrong file. Here is the 
correct one. Copy it to the same folder

https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m

On 5/13/2020 11:01 PM, Douglas N. Greve wrote:

Download this file
https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m
and copy it into $FREESURFER_HOME/matlab
and rerun. Let me know if that fixes it.

On 5/13/2020 5:57 PM, Angela Favaro wrote:

External Email - Use Caution

Please find attached the log
Thank you
Angela

Il giorno 13 mag 2020, alle ore 23:35, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

Are you running this from recon-all? If so send the recon-all.log. 
If from the command line, send the command-line and all terminal output

On 5/13/2020 5:28 PM, Angela Favaro wrote:

External Email - Use Caution

Hi Doug!
yes, it run under version 6!
Please let me know if it is something that can be solved
Thank you
Angela

Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

Does it run under version 6? We are not really supporting lGI 
anymore, but maybe we can get it to work

On 5/13/2020 4:24 PM, Angela Favaro wrote:

External Email - Use Caution

Hi all,
I am using the new version of Freesurfer 7.1.0
And I am finding problems in running gyrification analysis.
I have Matlab 2016a (and 2019b) with the toolbox image processing

The error is after the command find_corresponding_center_FSformat

Matlab seems to start, but then the following message appears:

>> Warning: Input argument must be a string.
> In ver (line 41)
In freesurfer_read_surf (line 70)
In find_corresponding_center_FSformat (line 26)
Error using fprintf
Function is not defined for 'struct' inputs.

Error in freesurfer_read_surf (line 70)
fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

Error in find_corresponding_center_FSformat (line 26)
[mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);

>> 
ERROR: find_corresponding_center_FSformat did not complete 
successfully!

I tried with both the Matlab version, but the error is the same
Any help is appreciated. Thank you so much

Angela

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Re: [Freesurfer] LGI problem

2020-05-13 Thread Douglas N. Greve

Download this file
https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m
and copy it into $FREESURFER_HOME/matlab
and rerun. Let me know if that fixes it.

On 5/13/2020 5:57 PM, Angela Favaro wrote:

External Email - Use Caution

Please find attached the log
Thank you
Angela

Il giorno 13 mag 2020, alle ore 23:35, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

Are you running this from recon-all? If so send the recon-all.log. If 
from the command line, send the command-line and all terminal output

On 5/13/2020 5:28 PM, Angela Favaro wrote:

External Email - Use Caution

Hi Doug!
yes, it run under version 6!
Please let me know if it is something that can be solved
Thank you
Angela

Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

Does it run under version 6? We are not really supporting lGI 
anymore, but maybe we can get it to work

On 5/13/2020 4:24 PM, Angela Favaro wrote:

External Email - Use Caution

Hi all,
I am using the new version of Freesurfer 7.1.0
And I am finding problems in running gyrification analysis.
I have Matlab 2016a (and 2019b) with the toolbox image processing

The error is after the command find_corresponding_center_FSformat

Matlab seems to start, but then the following message appears:

>> Warning: Input argument must be a string.
> In ver (line 41)
In freesurfer_read_surf (line 70)
In find_corresponding_center_FSformat (line 26)
Error using fprintf
Function is not defined for 'struct' inputs.

Error in freesurfer_read_surf (line 70)
fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

Error in find_corresponding_center_FSformat (line 26)
[mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);

>> 
ERROR: find_corresponding_center_FSformat did not complete 
successfully!

I tried with both the Matlab version, but the error is the same
Any help is appreciated. Thank you so much

Angela

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Re: [Freesurfer] LGI problem

2020-05-13 Thread Douglas N. Greve

Are you running this from recon-all? If so send the recon-all.log. If 
from the command line, send the command-line and all terminal output

On 5/13/2020 5:28 PM, Angela Favaro wrote:

External Email - Use Caution

Hi Doug!
yes, it run under version 6!
Please let me know if it is something that can be solved
Thank you
Angela

Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

Does it run under version 6? We are not really supporting lGI 
anymore, but maybe we can get it to work

On 5/13/2020 4:24 PM, Angela Favaro wrote:

External Email - Use Caution

Hi all,
I am using the new version of Freesurfer 7.1.0
And I am finding problems in running gyrification analysis.
I have Matlab 2016a (and 2019b) with the toolbox image processing

The error is after the command find_corresponding_center_FSformat

Matlab seems to start, but then the following message appears:

>> Warning: Input argument must be a string.
> In ver (line 41)
  In freesurfer_read_surf (line 70)
  In find_corresponding_center_FSformat (line 26)
Error using fprintf
Function is not defined for 'struct' inputs.

Error in freesurfer_read_surf (line 70)
fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

Error in find_corresponding_center_FSformat (line 26)
[mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);

>> 
ERROR: find_corresponding_center_FSformat did not complete successfully!

I tried with both the Matlab version, but the error is the same
Any help is appreciated. Thank you so much

Angela

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Re: [Freesurfer] LGI problem

2020-05-13 Thread Angela Favaro

External Email - Use Caution

Hi Doug!
yes, it run under version 6!
Please let me know if it is something that can be solved
Thank you
Angela


> Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve 
>  ha scritto:
> 
> Does it run under version 6? We are not really supporting lGI anymore, but 
> maybe we can get it to work
> 
> On 5/13/2020 4:24 PM, Angela Favaro wrote:
>> External Email - Use Caution
>> 
>> 
>> Hi all, 
>> I am using the new version of Freesurfer 7.1.0
>> And I am finding problems in running gyrification analysis.
>> I have Matlab 2016a (and 2019b) with the toolbox image processing
>> 
>> The error is after the command find_corresponding_center_FSformat
>> 
>> Matlab seems to start, but then the following message appears:
>> 
>> >> Warning: Input argument must be a string. 
>> > In ver (line 41)
>>   In freesurfer_read_surf (line 70)
>>   In find_corresponding_center_FSformat (line 26) 
>> Error using fprintf
>> Function is not defined for 'struct' inputs.
>> 
>> Error in freesurfer_read_surf (line 70)
>> fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));
>> 
>> Error in find_corresponding_center_FSformat (line 26)
>> [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);
>>  
>> >> 
>> ERROR: find_corresponding_center_FSformat did not complete successfully!
>> 
>> I tried with both the Matlab version, but the error is the same
>> Any help is appreciated. Thank you so much
>> 
>> Angela
>> 
>> 
>>> ___
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>>> 
>> 
>> 
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>> 
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Re: [Freesurfer] LGI problem

2020-05-13 Thread Douglas N. Greve

Does it run under version 6? We are not really supporting lGI anymore, 
but maybe we can get it to work

On 5/13/2020 4:24 PM, Angela Favaro wrote:

External Email - Use Caution

Hi all,
I am using the new version of Freesurfer 7.1.0
And I am finding problems in running gyrification analysis.
I have Matlab 2016a (and 2019b) with the toolbox image processing

The error is after the command find_corresponding_center_FSformat

Matlab seems to start, but then the following message appears:

>> Warning: Input argument must be a string.
> In ver (line 41)
  In freesurfer_read_surf (line 70)
  In find_corresponding_center_FSformat (line 26)
Error using fprintf
Function is not defined for 'struct' inputs.

Error in freesurfer_read_surf (line 70)
fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

Error in find_corresponding_center_FSformat (line 26)
[mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);

>> 
ERROR: find_corresponding_center_FSformat did not complete successfully!

I tried with both the Matlab version, but the error is the same
Any help is appreciated. Thank you so much

Angela

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[Freesurfer] LGI problem

2020-05-13 Thread Angela Favaro

External Email - Use Caution

Hi all,
I am using the new version of Freesurfer 7.1.0
And I am finding problems in running gyrification analysis.
I have Matlab 2016a (and 2019b) with the toolbox image processing

The error is after the command find_corresponding_center_FSformat

Matlab seems to start, but then the following message appears:

>> Warning: Input argument must be a string.
> In ver (line 41)
  In freesurfer_read_surf (line 70)
  In find_corresponding_center_FSformat (line 26)
Error using fprintf
Function is not defined for 'struct' inputs.

Error in freesurfer_read_surf (line 70)
fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

Error in find_corresponding_center_FSformat (line 26)
[mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);

>>
ERROR: find_corresponding_center_FSformat did not complete successfully!

I tried with both the Matlab version, but the error is the same
Any help is appreciated. Thank you so much

Angela


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[Freesurfer] LGI help

2020-03-03 Thread Nillo, Ryan Michael R

Hello Freesurfer users/developers,

I want to run recon-all localGI on a subject who has been processed with 
Freesurfer 5.3. Whenever I run recon-all -localGI, I always get an error on 
“make_roi_paths”. There error can be found at the end of this email. I looked 
at the 5.3 release notes and found the that one issue with localGI was fixed by 
substituting a line of code. The current SearchProjectionOnPial.m that I am 
using uses this fix.

LGI: issue when using Matlab 2013. the fix is to edit the file 
$FREESURFER_HOME/matlab/SearchProjectionOnPial.m and make these changes: 
find this line:

< for t=1:step:size(perim,2)

and change to:

> si=max(size(perim));
> for t=1:step:si




make_roi_paths('lh.pial','lh.pial-outer-smoothed',25,100,'/working/ABCD/FS/NDAR_INV021N0FLH/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrp_58433_.m');
 exit
=

< M A T L A B (R) >
  Copyright 1984-2015 The MathWorks, Inc.
   R2015b (8.6.0.267246) 64-bit (glnxa64)
  August 20, 2015
 
For online documentation, see http://www.mathworks.com/support
For product information, visit www.mathworks.com.
 

Academic License

>> loading datas ...
FREESURFER_READ_SURF [v  1.2 ]
...reading surface file: lh.pial
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done (  0.04 sec)

FREESURFER_READ_SURF [v  1.2 ]
...reading surface file: lh.pial-outer-smoothed
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done (  0.02 sec)

preparing outer mesh structure ...
face 5000 / 130188
face 1 / 130188
face 15000 / 130188
face 2 / 130188
face 25000 / 130188
face 3 / 130188
face 35000 / 130188
face 4 / 130188
face 45000 / 130188
face 5 / 130188
face 55000 / 130188
face 6 / 130188
face 65000 / 130188
face 7 / 130188
face 75000 / 130188
face 8 / 130188
face 85000 / 130188
face 9 / 130188
face 95000 / 130188
face 10 / 130188
face 105000 / 130188
face 11 / 130188
face 115000 / 130188
face 12 / 130188
face 125000 / 130188
face 13 / 130188

mesh_outer = 

 vertices: [65096x3 double]
faces: [130188x3 double]
facesOfVertex: [65096x1 struct]

preparing pial mesh structure ...
...searching for mesh edges...done (134.42 sec).
... creating path file for vertex 1 / 65096
area file for outer ROIs saved at 1
In an assignment  A(:) = B, the number of elements in A and B must be the same.

Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));

Error in mesh_vertex_nearest (line 29)
nearestIndex = dsearchn(vertices,points);


Error in reorganize_verticeslist (line 28)

[nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));

Error in make_roi_paths (line 93)
reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim,
verticeslist, step);
 
>> 
ERROR:  make_roi_paths did not complete successfully!
Linux jamestown.radiology.ucsf.edu 3.10.0-1062.1.2.el7.x86_64 #1 SMP Mon Sep 16 
14:19:51 EDT 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s NDAR_INV021N0FLH exited with ERRORS at Tue Mar  3 11:09:41 PST 2020

For more details, see the log file 
/working/ABCD/FS/NDAR_INV021N0FLH/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Thank you for your time,

Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging



smime.p7s
Description: S/MIME cryptographic signature
External Email - Use Caution___
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Re: [Freesurfer] LGI in QDEC menu please respond soon

External Email - Use Caution

I made a new qdec file in my subject directory (not capitalizing 'qdec')
and the problem was solved :)

Thank you so much. I really appreciate all your help

Avi

On Tue, Apr 23, 2019 at 2:57 PM Pan Yunzhi  wrote:

> External Email - Use Caution
>
> You should edit your .Qdecrc file in your  SUBJECTS_DIR/qdec
>   folder. Don't capitalize qdec.
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Avi Gharehgazlou 
> *Sent: *Tuesday, April 23, 2019 2:27 PM
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] LGI in QDEC menu please respond soon
>
>
>
> *External Email - Use Caution*
>
> Where should I type "ctrl +H"? In my linux terminal (in QDEC) folder? when
> I do that it gives this error: bash: ctrl + H: command not found
>
>
>
> When I open my .Qdecrc file (with geddit) I see the MEASURE1 = pial_lgi in
> the file (but not all the other lines that came in the output when I wrote
> command more ~/.Qdecrc)
>
>
>
> On Tue, Apr 23, 2019 at 1:38 PM Pan Yunzhi  wrote:
>
> *External Email - Use Caution*
>
> I guess the .Qdecrc file have already in your qdec folder. Try “ctrl + H”
> to see the hiden file and write MEASURE1 = pial_lgi into .Qdecrc file.
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Avi Gharehgazlou 
> *Sent: *Tuesday, April 23, 2019 1:34 PM
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] LGI in QDEC menu please respond soon
>
>
>
> *External Email - Use Caution*
>
> Yes I did
>
>
>
> On Tue, Apr 23, 2019 at 12:59 PM Pan Yunzhi  wrote:
>
> *External Email - Use Caution*
>
> Did you run this command “recon-all -s my_subject_id -qcache -measure
> pial_lgi” before？ If not， you should run this.
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Avi Gharehgazlou 
> *Sent: *Tuesday, April 23, 2019 12:06 PM
> *To: *Freesurfer support list 
> *Subject: *[Freesurfer] LGI in QDEC menu please respond soon
>
>
>
> *External Email - Use Caution*
>
> Hi experts,
>
> To give more detail re my previous post  I have created the .Qdecrc
> file in my Subjects directory and QDEC folder, which contains one line
> : MEASURE1 = pial_lgi . However, LGI is still not appearing in the drop
> down menu on QDEC.
>
>
>
> When I do command more ~/.Qdecrc it gives the following output:
>
>
>
>
>
> # 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+531+190
>
> Qdec1\RunTime\MostRecentVersionLaunched = 1.5
>
> Qdec1\RunTime\PrintTargetDPI = 100.00
>
> Qdec1\RunTime\ShowBalloonHelp = 1
>
> Qdec1\RunTime\ShowSplashScreen = 1
>
> Qdec1\RunTime\ToolbarFlatButtons = 1
>
> Qdec1\RunTime\ToolbarFlatFrame = 1
>
>
>
> Based on previous archives I think my .Qdecrc was not saved properly
> because the line in this file (MEASURE1 = pial_lgi) doesn't appear in the
> above output. I know I have to put this line in the above output, but I
> can't seem to figure out how. Will you please be able to tell me how I can
> do this?
>
> Thanks so much
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] LGI in QDEC menu please respond soon

External Email - Use Caution

You should edit your .Qdecrc file in your  SUBJECTS_DIR/qdec   
folder. Don't capitalize qdec. 

Sent from Mail for Windows 10

From: Avi Gharehgazlou
Sent: Tuesday, April 23, 2019 2:27 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] LGI in QDEC menu please respond soon

External Email - Use Caution
Where should I type "ctrl +H"? In my linux terminal (in QDEC) folder? when I do 
that it gives this error: bash: ctrl + H: command not found

When I open my .Qdecrc file (with geddit) I see the MEASURE1 = pial_lgi in the 
file (but not all the other lines that came in the output when I wrote command 
more ~/.Qdecrc)

On Tue, Apr 23, 2019 at 1:38 PM Pan Yunzhi  wrote:
External Email - Use Caution
I guess the .Qdecrc file have already in your qdec folder. Try “ctrl + H” to 
see the hiden file and write MEASURE1 = pial_lgi into .Qdecrc file.

Sent from Mail for Windows 10

From: Avi Gharehgazlou
Sent: Tuesday, April 23, 2019 1:34 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] LGI in QDEC menu please respond soon

External Email - Use Caution
Yes I did

On Tue, Apr 23, 2019 at 12:59 PM Pan Yunzhi  wrote:
External Email - Use Caution
Did you run this command “recon-all -s my_subject_id -qcache -measure pial_lgi” 
before？ If not， you should run this.

Sent from Mail for Windows 10

From: Avi Gharehgazlou
Sent: Tuesday, April 23, 2019 12:06 PM
To: Freesurfer support list
Subject: [Freesurfer] LGI in QDEC menu please respond soon

External Email - Use Caution
Hi experts, 
To give more detail re my previous post  I have created the .Qdecrc file in 
my Subjects directory and QDEC folder, which contains one line : MEASURE1 = 
pial_lgi . However, LGI is still not appearing in the drop down menu on QDEC. 

When I do command more ~/.Qdecrc it gives the following output:

# 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+531+190
Qdec1\RunTime\MostRecentVersionLaunched = 1.5
Qdec1\RunTime\PrintTargetDPI = 100.00
Qdec1\RunTime\ShowBalloonHelp = 1
Qdec1\RunTime\ShowSplashScreen = 1
Qdec1\RunTime\ToolbarFlatButtons = 1
Qdec1\RunTime\ToolbarFlatFrame = 1

Based on previous archives I think my .Qdecrc was not saved properly because 
the line in this file (MEASURE1 = pial_lgi) doesn't appear in the above output. 
I know I have to put this line in the above output, but I can't seem to figure 
out how. Will you please be able to tell me how I can do this?
Thanks so much  

___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] LGI in QDEC menu please respond soon

External Email - Use Caution

In .Qdecrc file, you can only see this line, except you add somethings else. If 
all of these were settled down, it should work. Is there any error in your 
command windows? 

Sent from Mail for Windows 10

From: Avi Gharehgazlou
Sent: Tuesday, April 23, 2019 2:27 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] LGI in QDEC menu please respond soon

External Email - Use Caution
Where should I type "ctrl +H"? In my linux terminal (in QDEC) folder? when I do 
that it gives this error: bash: ctrl + H: command not found

When I open my .Qdecrc file (with geddit) I see the MEASURE1 = pial_lgi in the 
file (but not all the other lines that came in the output when I wrote command 
more ~/.Qdecrc)

On Tue, Apr 23, 2019 at 1:38 PM Pan Yunzhi  wrote:
External Email - Use Caution
I guess the .Qdecrc file have already in your qdec folder. Try “ctrl + H” to 
see the hiden file and write MEASURE1 = pial_lgi into .Qdecrc file.
 
Sent from Mail for Windows 10
 
From: Avi Gharehgazlou
Sent: Tuesday, April 23, 2019 1:34 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] LGI in QDEC menu please respond soon
 
External Email - Use Caution
Yes I did
 
On Tue, Apr 23, 2019 at 12:59 PM Pan Yunzhi  wrote:
External Email - Use Caution
Did you run this command “recon-all -s my_subject_id -qcache -measure pial_lgi” 
before？ If not， you should run this.
 
Sent from Mail for Windows 10
 
From: Avi Gharehgazlou
Sent: Tuesday, April 23, 2019 12:06 PM
To: Freesurfer support list
Subject: [Freesurfer] LGI in QDEC menu please respond soon
 
External Email - Use Caution
Hi experts, 
To give more detail re my previous post  I have created the .Qdecrc file in 
my Subjects directory and QDEC folder, which contains one line : MEASURE1 = 
pial_lgi . However, LGI is still not appearing in the drop down menu on QDEC. 
 
When I do command more ~/.Qdecrc it gives the following output:
 
 
# 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+531+190
Qdec1\RunTime\MostRecentVersionLaunched = 1.5
Qdec1\RunTime\PrintTargetDPI = 100.00
Qdec1\RunTime\ShowBalloonHelp = 1
Qdec1\RunTime\ShowSplashScreen = 1
Qdec1\RunTime\ToolbarFlatButtons = 1
Qdec1\RunTime\ToolbarFlatFrame = 1
 
Based on previous archives I think my .Qdecrc was not saved properly because 
the line in this file (MEASURE1 = pial_lgi) doesn't appear in the above output. 
I know I have to put this line in the above output, but I can't seem to figure 
out how. Will you please be able to tell me how I can do this?
Thanks so much  
 
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] LGI in QDEC menu please respond soon

External Email - Use Caution

Where should I type "ctrl +H"? In my linux terminal (in QDEC) folder? when
I do that it gives this error: bash: ctrl + H: command not found

When I open my .Qdecrc file (with geddit) I see the MEASURE1 = pial_lgi in
the file (but not all the other lines that came in the output when I wrote
command more ~/.Qdecrc)

On Tue, Apr 23, 2019 at 1:38 PM Pan Yunzhi  wrote:

> External Email - Use Caution
>
> I guess the .Qdecrc file have already in your qdec folder. Try “ctrl + H”
> to see the hiden file and write MEASURE1 = pial_lgi into .Qdecrc file.
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Avi Gharehgazlou 
> *Sent: *Tuesday, April 23, 2019 1:34 PM
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] LGI in QDEC menu please respond soon
>
>
>
> *External Email - Use Caution*
>
> Yes I did
>
>
>
> On Tue, Apr 23, 2019 at 12:59 PM Pan Yunzhi  wrote:
>
> *External Email - Use Caution*
>
> Did you run this command “recon-all -s my_subject_id -qcache -measure
> pial_lgi” before？ If not， you should run this.
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Avi Gharehgazlou 
> *Sent: *Tuesday, April 23, 2019 12:06 PM
> *To: *Freesurfer support list 
> *Subject: *[Freesurfer] LGI in QDEC menu please respond soon
>
>
>
> *External Email - Use Caution*
>
> Hi experts,
>
> To give more detail re my previous post  I have created the .Qdecrc
> file in my Subjects directory and QDEC folder, which contains one line
> : MEASURE1 = pial_lgi . However, LGI is still not appearing in the drop
> down menu on QDEC.
>
>
>
> When I do command more ~/.Qdecrc it gives the following output:
>
>
>
>
>
> # 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+531+190
>
> Qdec1\RunTime\MostRecentVersionLaunched = 1.5
>
> Qdec1\RunTime\PrintTargetDPI = 100.00
>
> Qdec1\RunTime\ShowBalloonHelp = 1
>
> Qdec1\RunTime\ShowSplashScreen = 1
>
> Qdec1\RunTime\ToolbarFlatButtons = 1
>
> Qdec1\RunTime\ToolbarFlatFrame = 1
>
>
>
> Based on previous archives I think my .Qdecrc was not saved properly
> because the line in this file (MEASURE1 = pial_lgi) doesn't appear in the
> above output. I know I have to put this line in the above output, but I
> can't seem to figure out how. Will you please be able to tell me how I can
> do this?
>
> Thanks so much
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] LGI in QDEC menu please respond soon

External Email - Use Caution

I guess the .Qdecrc file have already in your qdec folder. Try “ctrl + H” to 
see the hiden file and write MEASURE1 = pial_lgi into .Qdecrc file.

Sent from Mail for Windows 10

From: Avi Gharehgazlou
Sent: Tuesday, April 23, 2019 1:34 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] LGI in QDEC menu please respond soon

External Email - Use Caution
Yes I did

On Tue, Apr 23, 2019 at 12:59 PM Pan Yunzhi  wrote:
External Email - Use Caution
Did you run this command “recon-all -s my_subject_id -qcache -measure pial_lgi” 
before？ If not， you should run this.

Sent from Mail for Windows 10

From: Avi Gharehgazlou
Sent: Tuesday, April 23, 2019 12:06 PM
To: Freesurfer support list
Subject: [Freesurfer] LGI in QDEC menu please respond soon

External Email - Use Caution
Hi experts, 
To give more detail re my previous post  I have created the .Qdecrc file in 
my Subjects directory and QDEC folder, which contains one line : MEASURE1 = 
pial_lgi . However, LGI is still not appearing in the drop down menu on QDEC. 

When I do command more ~/.Qdecrc it gives the following output:

# 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+531+190
Qdec1\RunTime\MostRecentVersionLaunched = 1.5
Qdec1\RunTime\PrintTargetDPI = 100.00
Qdec1\RunTime\ShowBalloonHelp = 1
Qdec1\RunTime\ShowSplashScreen = 1
Qdec1\RunTime\ToolbarFlatButtons = 1
Qdec1\RunTime\ToolbarFlatFrame = 1

Based on previous archives I think my .Qdecrc was not saved properly because 
the line in this file (MEASURE1 = pial_lgi) doesn't appear in the above output. 
I know I have to put this line in the above output, but I can't seem to figure 
out how. Will you please be able to tell me how I can do this?
Thanks so much  

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] LGI in QDEC menu please respond soon

External Email - Use Caution

Yes I did

On Tue, Apr 23, 2019 at 12:59 PM Pan Yunzhi  wrote:

> External Email - Use Caution
>
> Did you run this command “recon-all -s my_subject_id -qcache -measure
> pial_lgi” before？ If not， you should run this.
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Avi Gharehgazlou 
> *Sent: *Tuesday, April 23, 2019 12:06 PM
> *To: *Freesurfer support list 
> *Subject: *[Freesurfer] LGI in QDEC menu please respond soon
>
>
>
> *External Email - Use Caution*
>
> Hi experts,
>
> To give more detail re my previous post  I have created the .Qdecrc
> file in my Subjects directory and QDEC folder, which contains one line
> : MEASURE1 = pial_lgi . However, LGI is still not appearing in the drop
> down menu on QDEC.
>
>
>
> When I do command more ~/.Qdecrc it gives the following output:
>
>
>
>
>
> # 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+531+190
>
> Qdec1\RunTime\MostRecentVersionLaunched = 1.5
>
> Qdec1\RunTime\PrintTargetDPI = 100.00
>
> Qdec1\RunTime\ShowBalloonHelp = 1
>
> Qdec1\RunTime\ShowSplashScreen = 1
>
> Qdec1\RunTime\ToolbarFlatButtons = 1
>
> Qdec1\RunTime\ToolbarFlatFrame = 1
>
>
>
> Based on previous archives I think my .Qdecrc was not saved properly
> because the line in this file (MEASURE1 = pial_lgi) doesn't appear in the
> above output. I know I have to put this line in the above output, but I
> can't seem to figure out how. Will you please be able to tell me how I can
> do this?
>
> Thanks so much
>
>
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Re: [Freesurfer] LGI in QDEC menu please respond soon

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Did you run this command “recon-all -s my_subject_id -qcache -measure pial_lgi” 
before？ If not， you should run this.

Sent from Mail for Windows 10

From: Avi Gharehgazlou
Sent: Tuesday, April 23, 2019 12:06 PM
To: Freesurfer support list
Subject: [Freesurfer] LGI in QDEC menu please respond soon

External Email - Use Caution
Hi experts, 
To give more detail re my previous post  I have created the .Qdecrc file in 
my Subjects directory and QDEC folder, which contains one line : MEASURE1 = 
pial_lgi . However, LGI is still not appearing in the drop down menu on QDEC. 

When I do command more ~/.Qdecrc it gives the following output:

# 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+531+190
Qdec1\RunTime\MostRecentVersionLaunched = 1.5
Qdec1\RunTime\PrintTargetDPI = 100.00
Qdec1\RunTime\ShowBalloonHelp = 1
Qdec1\RunTime\ShowSplashScreen = 1
Qdec1\RunTime\ToolbarFlatButtons = 1
Qdec1\RunTime\ToolbarFlatFrame = 1

Based on previous archives I think my .Qdecrc was not saved properly because 
the line in this file (MEASURE1 = pial_lgi) doesn't appear in the above output. 
I know I have to put this line in the above output, but I can't seem to figure 
out how. Will you please be able to tell me how I can do this?
Thanks so much  

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[Freesurfer] LGI in QDEC menu please respond soon