Re: [Freesurfer] IndexError: list index out of range

[Makaretz, Sara Johanna]

Resolved - thank you Andrew!


Solution: operator error, needed to cat file w/ input list for --inputs instead 
of just specifying file w/ input list


From: Hoopes, Andrew
Sent: Thursday, February 15, 2018 4:43:18 PM
To: Makaretz, Sara Johanna; Freesurfer support list
Subject: Re: [Freesurfer] IndexError: list index out of range

Thanks Sarah, I haven’t been able to replicate this - do you mind sending the 
stats file that you’re using as input?

Andrew



On February 15, 2018 at 3:58:17 PM, Makaretz, Sara Johanna 
(smakar...@mgh.harvard.edu<mailto:smakar...@mgh.harvard.edu>) wrote:

Hi Andrew,

python --version
=
Python 2.7.3 -- EPD 7.3-1 (64-bit)

Sara


From: Hoopes, Andrew
Sent: Thursday, February 15, 2018 3:56:22 PM
To: Makaretz, Sara Johanna; Freesurfer support list
Subject: Re: [Freesurfer] IndexError: list index out of range

Hi Sara and Arkadiy,

What version of python2 are you using?
python --version

thanks
Andrew


On February 13, 2018 at 10:16:34 AM, Makaretz, Sara Johanna 
(smakar...@mgh.harvard.edu<mailto:smakar...@mgh.harvard.edu>) wrote:

*I also got this error when I ran w/ python 2:


python2 $FREESURFER_HOME/bin/asegstats2table --common-segs -t 
aparc.a2009s+aseg.max.table -i aparc.a2009s+aseg.lst -m max

Parsing the .stats files
Traceback (most recent call last):
  File "/usr/local/freesurfer/stable6/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)
  File "/autofs/cluster/freesurfer/centos7_x86_64/stable6/bin/fsutils.py", line 
115, in parse
seg = strlst[1] # segmentation id is in the 2nd field
IndexError: list index out of range



From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Makaretz, Sara Johanna 
<smakar...@mgh.harvard.edu>
Sent: Tuesday, February 13, 2018 10:12:07 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] IndexError: list index out of range


Hi Doug,


I am also getting the error "IndexError: list index out of range" - I got the 
same error using FS6.0/FS5.3/dev. This is what I'm running for asegstats2table:


asegstats2table --common-segs -t aparc.a2009s+aseg.max.table -i 
aparc.a2009s+aseg.lst -m max

Parsing the .stats files
Traceback (most recent call last):
  File "/usr/local/freesurfer/stable6/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)
  File "/autofs/cluster/freesurfer/centos7_x86_64/stable6/bin/fsutils.py", line 
115, in parse
seg = strlst[1] # segmentation id is in the 2nd field
IndexError: list index out of range

This is what I ran to make my stats files, which look fine:
mri_label2vol --seg aparc.a2009s+aseg.nii --temp pet.nii --o 
ns_aparc.a2009s+aseg.nii --reg anat2pet.lta
mri_segstats --seg ns_aparc.a2009s+aseg.nii --i pet.nii --sum 
aparc.a2009s+aseg.stats


Do you have any tips on getting this working?


Thanks in advance for any help!

Sara


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Maksimovskiy, Arkadiy 
<amaksimovs...@mclean.harvard.edu>
Sent: Monday, January 8, 2018 11:50:42 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] IndexError: list index out of range


Hi Doug,



I sent you the tar files, but just wanted to update you that I tried running 
this with just one subjects and am still getting an error but a different one. 
The two inputs and output errors in the terminal are pasted below:



[arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits]
 amaksimovskiy% asegstats2table --subjects SILVA030  --meas volume --stats 
aseg.stats --tablefile Subcortical_GM_Volume1.Dec17.txt

SUBJECTS_DIR : 
/Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits

Parsing the .stats files

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)

  File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse

seg = strlst[1] # segmentation id is in the 2nd field

IndexError: list index out of range

[arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits]
 amaksimovskiy% asegstats2table --subjects SILVA040  --meas volume --stats 
aseg.stats --tablefile Subcortical_GM_Volume1.Dec17.txt

SUBJECTS_DIR : 
/Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits

Parsing the .stats files

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)

  File "/Applications/freesurfer/bin/fsutils.py", line 122, in parse

s

Re: [Freesurfer] IndexError: list index out of range

[Makaretz, Sara Johanna]

Hi Andrew,

python --version
=
Python 2.7.3 -- EPD 7.3-1 (64-bit)

Sara



From: Hoopes, Andrew
Sent: Thursday, February 15, 2018 3:56:22 PM
To: Makaretz, Sara Johanna; Freesurfer support list
Subject: Re: [Freesurfer] IndexError: list index out of range

Hi Sara and Arkadiy,

What version of python2 are you using?
python --version

thanks
Andrew


On February 13, 2018 at 10:16:34 AM, Makaretz, Sara Johanna 
(smakar...@mgh.harvard.edu<mailto:smakar...@mgh.harvard.edu>) wrote:

*I also got this error when I ran w/ python 2:


python2 $FREESURFER_HOME/bin/asegstats2table --common-segs -t 
aparc.a2009s+aseg.max.table -i aparc.a2009s+aseg.lst -m max

Parsing the .stats files
Traceback (most recent call last):
  File "/usr/local/freesurfer/stable6/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)
  File "/autofs/cluster/freesurfer/centos7_x86_64/stable6/bin/fsutils.py", line 
115, in parse
seg = strlst[1] # segmentation id is in the 2nd field
IndexError: list index out of range



From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Makaretz, Sara Johanna 
<smakar...@mgh.harvard.edu>
Sent: Tuesday, February 13, 2018 10:12:07 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] IndexError: list index out of range


Hi Doug,


I am also getting the error "IndexError: list index out of range" - I got the 
same error using FS6.0/FS5.3/dev. This is what I'm running for asegstats2table:


asegstats2table --common-segs -t aparc.a2009s+aseg.max.table -i 
aparc.a2009s+aseg.lst -m max

Parsing the .stats files
Traceback (most recent call last):
  File "/usr/local/freesurfer/stable6/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)
  File "/autofs/cluster/freesurfer/centos7_x86_64/stable6/bin/fsutils.py", line 
115, in parse
seg = strlst[1] # segmentation id is in the 2nd field
IndexError: list index out of range

This is what I ran to make my stats files, which look fine:
mri_label2vol --seg aparc.a2009s+aseg.nii --temp pet.nii --o 
ns_aparc.a2009s+aseg.nii --reg anat2pet.lta
mri_segstats --seg ns_aparc.a2009s+aseg.nii --i pet.nii --sum 
aparc.a2009s+aseg.stats


Do you have any tips on getting this working?


Thanks in advance for any help!

Sara


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Maksimovskiy, Arkadiy 
<amaksimovs...@mclean.harvard.edu>
Sent: Monday, January 8, 2018 11:50:42 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] IndexError: list index out of range


Hi Doug,



I sent you the tar files, but just wanted to update you that I tried running 
this with just one subjects and am still getting an error but a different one. 
The two inputs and output errors in the terminal are pasted below:



[arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits]
 amaksimovskiy% asegstats2table --subjects SILVA030  --meas volume --stats 
aseg.stats --tablefile Subcortical_GM_Volume1.Dec17.txt

SUBJECTS_DIR : 
/Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits

Parsing the .stats files

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)

  File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse

seg = strlst[1] # segmentation id is in the 2nd field

IndexError: list index out of range

[arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits]
 amaksimovskiy% asegstats2table --subjects SILVA040  --meas volume --stats 
aseg.stats --tablefile Subcortical_GM_Volume1.Dec17.txt

SUBJECTS_DIR : 
/Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits

Parsing the .stats files

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)

  File "/Applications/freesurfer/bin/fsutils.py", line 122, in parse

self.measurelist.append( float(strlst[self.measure_column_map[measure]] ))

ValueError: could not convert string to float: Left-Cerebellum-Cortex





Let me know if any further info is needed to troubleshoot. Thank you for 
helping with this.

-arkadiy



--

Arkadiy L. Maksimovskiy, Ph.D.

Postdoctoral Research Fellow
McLean Imaging Center, McLean Hospital
Department of Psychiatry, Harvard Medical School

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

Re: [Freesurfer] IndexError: list index out of range

[Makaretz, Sara Johanna]

*I also got this error when I ran w/ python 2:


python2 $FREESURFER_HOME/bin/asegstats2table --common-segs -t 
aparc.a2009s+aseg.max.table -i aparc.a2009s+aseg.lst -m max

Parsing the .stats files
Traceback (most recent call last):
  File "/usr/local/freesurfer/stable6/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)
  File "/autofs/cluster/freesurfer/centos7_x86_64/stable6/bin/fsutils.py", line 
115, in parse
seg = strlst[1] # segmentation id is in the 2nd field
IndexError: list index out of range




From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Makaretz, Sara Johanna 
<smakar...@mgh.harvard.edu>
Sent: Tuesday, February 13, 2018 10:12:07 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] IndexError: list index out of range


Hi Doug,


I am also getting the error "IndexError: list index out of range" - I got the 
same error using FS6.0/FS5.3/dev. This is what I'm running for asegstats2table:


asegstats2table --common-segs -t aparc.a2009s+aseg.max.table -i 
aparc.a2009s+aseg.lst -m max

Parsing the .stats files
Traceback (most recent call last):
  File "/usr/local/freesurfer/stable6/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)
  File "/autofs/cluster/freesurfer/centos7_x86_64/stable6/bin/fsutils.py", line 
115, in parse
seg = strlst[1] # segmentation id is in the 2nd field
IndexError: list index out of range

This is what I ran to make my stats files, which look fine:
mri_label2vol --seg aparc.a2009s+aseg.nii --temp pet.nii --o 
ns_aparc.a2009s+aseg.nii --reg anat2pet.lta
mri_segstats --seg ns_aparc.a2009s+aseg.nii --i pet.nii --sum 
aparc.a2009s+aseg.stats


Do you have any tips on getting this working?


Thanks in advance for any help!

Sara


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Maksimovskiy, Arkadiy 
<amaksimovs...@mclean.harvard.edu>
Sent: Monday, January 8, 2018 11:50:42 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] IndexError: list index out of range


Hi Doug,



I sent you the tar files, but just wanted to update you that I tried running 
this with just one subjects and am still getting an error but a different one. 
The two inputs and output errors in the terminal are pasted below:



[arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits]
 amaksimovskiy% asegstats2table --subjects SILVA030  --meas volume --stats 
aseg.stats --tablefile Subcortical_GM_Volume1.Dec17.txt

SUBJECTS_DIR : 
/Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits

Parsing the .stats files

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)

  File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse

seg = strlst[1] # segmentation id is in the 2nd field

IndexError: list index out of range

[arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits]
 amaksimovskiy% asegstats2table --subjects SILVA040  --meas volume --stats 
aseg.stats --tablefile Subcortical_GM_Volume1.Dec17.txt

SUBJECTS_DIR : 
/Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits

Parsing the .stats files

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)

  File "/Applications/freesurfer/bin/fsutils.py", line 122, in parse

self.measurelist.append( float(strlst[self.measure_column_map[measure]] ))

ValueError: could not convert string to float: Left-Cerebellum-Cortex





Let me know if any further info is needed to troubleshoot. Thank you for 
helping with this.

-arkadiy



--

Arkadiy L. Maksimovskiy, Ph.D.

Postdoctoral Research Fellow
McLean Imaging Center, McLean Hospital
Department of Psychiatry, Harvard Medical School
___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] IndexError: list index out of range

[Makaretz, Sara Johanna]

Hi Doug,


I am also getting the error "IndexError: list index out of range" - I got the 
same error using FS6.0/FS5.3/dev. This is what I'm running for asegstats2table:


asegstats2table --common-segs -t aparc.a2009s+aseg.max.table -i 
aparc.a2009s+aseg.lst -m max

Parsing the .stats files
Traceback (most recent call last):
  File "/usr/local/freesurfer/stable6/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)
  File "/autofs/cluster/freesurfer/centos7_x86_64/stable6/bin/fsutils.py", line 
115, in parse
seg = strlst[1] # segmentation id is in the 2nd field
IndexError: list index out of range

This is what I ran to make my stats files, which look fine:
mri_label2vol --seg aparc.a2009s+aseg.nii --temp pet.nii --o 
ns_aparc.a2009s+aseg.nii --reg anat2pet.lta
mri_segstats --seg ns_aparc.a2009s+aseg.nii --i pet.nii --sum 
aparc.a2009s+aseg.stats


Do you have any tips on getting this working?


Thanks in advance for any help!

Sara


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maksimovskiy, Arkadiy 

Sent: Monday, January 8, 2018 11:50:42 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] IndexError: list index out of range


Hi Doug,



I sent you the tar files, but just wanted to update you that I tried running 
this with just one subjects and am still getting an error but a different one. 
The two inputs and output errors in the terminal are pasted below:



[arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits]
 amaksimovskiy% asegstats2table --subjects SILVA030  --meas volume --stats 
aseg.stats --tablefile Subcortical_GM_Volume1.Dec17.txt

SUBJECTS_DIR : 
/Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits

Parsing the .stats files

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)

  File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse

seg = strlst[1] # segmentation id is in the 2nd field

IndexError: list index out of range

[arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits]
 amaksimovskiy% asegstats2table --subjects SILVA040  --meas volume --stats 
aseg.stats --tablefile Subcortical_GM_Volume1.Dec17.txt

SUBJECTS_DIR : 
/Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits

Parsing the .stats files

Traceback (most recent call last):

  File "/Applications/freesurfer/bin/asegstats2table", line 548, in 

id_name_map, measurelist = parsed.parse(options.meas)

  File "/Applications/freesurfer/bin/fsutils.py", line 122, in parse

self.measurelist.append( float(strlst[self.measure_column_map[measure]] ))

ValueError: could not convert string to float: Left-Cerebellum-Cortex





Let me know if any further info is needed to troubleshoot. Thank you for 
helping with this.

-arkadiy



--

Arkadiy L. Maksimovskiy, Ph.D.

Postdoctoral Research Fellow
McLean Imaging Center, McLean Hospital
Department of Psychiatry, Harvard Medical School
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

[Freesurfer] # voxels above thresholds across aparc+aseg regions - mri_segstats?

[Makaretz, Sara Johanna]

Hi FS group,


My goal is to calculate the % of voxels in a given region that are higher than 
a region-specific threshold. This is what I've done so far for each subject:


  *   recon T1
  *   coregister vol.nii to T1
  *   move aparc+aseg.mgz into functional space
  *   mri_segstats --i vol.nii --seg aparc+aseg.functionalspace.nii --sum 
vol.aparc+aseg.stats   to get NVoxels & mean stats


For each subject, for each cortical region (Seg1001-1035 & Seg2001-2035), I now 
want to count the number of voxels that are above region-specific thresholds as 
found in thresh.lst, ie.


  ctx-lh-banksstsSeg10011.383697722
  ctx-lh-caudalanteriorcingulateSeg10021.272858762
  ctx-lh-caudalmiddlefrontalSeg10031.167540497
  ...


Do you have any advice on the best way to do this? I think I can use 
mri_segstats, but am not sure if I'm looking at the right arguments and/or if 
there is a more straightforward way to do this. This is what I have so far:


  foreach s (`cat s.lst`)   /   foreach seg (`cat thresh.lst | awk '{print 
$2}'`)

  set thresh = `cat thresh.lst | grep $seg | awk '{print $3}'`

  mri_segstats --i vol.nii --seg aparc+aseg.functionalspace.nii --id $seg 
--maskthresh $thresh --masksign pos --sum tmp.$seg.stats

  ...and then grep NVoxels from tmp.$seg.stats, grep total NVoxels from 
vol.aparc+aseg.stats, divide/echo into summary stats file?



Thank you in advance for any advice!


Best,

Sara

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

Re: [Freesurfer] mri_gtmpvc & mri_gtmseg errors - failed tissue type check

[Makaretz, Sara Johanna]

Hi Doug,


I'm still stuck on this subject and am wondering if you have any advice.


Thanks for any help!

Sara



From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Makaretz, Sara Johanna 
<smakar...@mgh.harvard.edu>
Sent: Friday, December 15, 2017 12:04:48 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_gtmpvc & mri_gtmseg errors - failed tissue type check

Hi Doug,

I ran mri_gtmseg on a subject & got no errors, and the gtmseg.mgz/apas+head.mgz 
outputs looked fine:
$Id: mri_gtmseg.c,v 1.9.2.1 2016/08/02 21:07:49 greve Exp $
mri_gtmseg --s $s
etc, exited fine

Then I tried running mri_gtmpvc, and got a 'failed tissue type check' error:
[weckl:FDG_2017-11-15] (nmr-stable6-env) cat 
MR_2017-11-07/pvc.psf06/mri_gtmpvc.log
$Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $
setenv SUBJECTS_DIR $SUBJECTS_DIR
mri_gtmpvc --auto-mask 11 .001 --rbv --mgx .25 --lgtm --threads 8 --seg 
gtmseg.mgz --no-rescale --save-input --i $PET_DIR/MeanPET.nii --reg 
$PET_DIR/reg.pet2t1.lta --psf 6 --o $PET_DIR/pvc.psf06 --default-seg-merge
sysname  Linux
hostname weckl.nmr.mgh.harvard.edu
machine  x86_64
user makaretz
vgthresh   0.001000
nReplace   18
0. 0. 0. 0. 0. 0.
Loading seg for gtm $SUBJECTS_DIR/$s/mri/gtmseg.mgz
Loading ctab $SUBJECTS_DIR/$s/mri/gtmseg.ctab
Reading $SUBJECTS_DIR/$s/mri/gtmseg.lta
Failed tissue type check
[weckl:FDG_2017-11-15] (nmr-stable6-env)

I tried re-running mri_gtmseg and adding --keep-cc, as recommended in this 
thread (I left out --no-xcerseg since I think it's now the default): 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-January/043523.html 
But I got a different error, where it's trying to write to a file called (null):
[weckl:FDG_2017-11-15] (nmr-stable6-env) mri_gtmseg --s $s --keep-cc
$Id: mri_gtmseg.c,v 1.9.2.1 2016/08/02 21:07:49 greve Exp $
cwd $PET_DIR
cmdline mri_gtmseg --s $s--keep-cc
sysname  Linux
hostname weckl.nmr.mgh.harvard.edu
machine  x86_64
user makaretz
subject $s
USF 2
OutputUSF 2
apasfile apas+head.mgz
wmannotfile NULL
ctxannotfile aparc.annot
ctxlhbase 1000
ctxrhbase 2000
SubSegWM   0
KeepHypo   0
KeepCC   1
dmax 5.00
nlist   0
lhmin  1000
lhmax  1900
rhmin  2000
rhmax  2900
Starting MRIgtmSeg()
Starting MRIgtmSeg() USF=2
Loading $SUBJECTS_DIR/$s/mri/apas+head.mgz
Loading surfaces  t = 2.1280
Loading annotations  t = 6.2390
Not segmenting WM
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
 Relabeling any unlateralized hypointenities as lateralized hypointenities
  MRIrelabelHypoHemi(): looping over volume
 nthreads = 1
 Relabeling any hypointensities as WM
  MRIunsegmentWM(): looping over volume
 nthreads = 1
Upsampling segmentation USF = 2 t = 32.3010
  MRIhiresSeg(): filling unknowns with 257
Beginning cortical segmentation using aparc.annot t = 83.9890
  MRIannot2CorticalSeg(): looping over volume
 nthreads = 1
  MRIannot2CorticalSeg(): found 1517 unknown, filled with 257
Not subsegmenting WM
Found 115 segs in the final list
MRIgtmSeg() done, t = 358.8340
Computing colortable
WARNING: segid   29 Left-undetermined tissue type is not set
Writing output file to $SUBJECTS_DIR/$s/mri/(null)
unknown file type for file ($SUBJECTS_DIR/$s/mri/(null))
[weckl:FDG_2017-11-15] (nmr-stable6-env)
[Freesurfer] Reading values from overlays with 
PETcoreg<https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-January/043523.html>
mail.nmr.mgh.harvard.edu
The problem is that --default-seg-merge merges the CC with WM, so you can't use 
that option, which means that you'll have to specify the rest of the default 
seg merge ...


I think I ruled out the usual operator errors (typos/SUBJECTS_DIR/permissions). 
Do you have any advice?

Thank you in advance for any help!
Sara
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[Freesurfer] mri_gtmpvc & mri_gtmseg errors - failed tissue type check

[Makaretz, Sara Johanna]

Hi Doug,

I ran mri_gtmseg on a subject & got no errors, and the gtmseg.mgz/apas+head.mgz 
outputs looked fine:
$Id: mri_gtmseg.c,v 1.9.2.1 2016/08/02 21:07:49 greve Exp $
mri_gtmseg --s $s
etc, exited fine

Then I tried running mri_gtmpvc, and got a 'failed tissue type check' error:
[weckl:FDG_2017-11-15] (nmr-stable6-env) cat 
MR_2017-11-07/pvc.psf06/mri_gtmpvc.log
$Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $
setenv SUBJECTS_DIR $SUBJECTS_DIR
mri_gtmpvc --auto-mask 11 .001 --rbv --mgx .25 --lgtm --threads 8 --seg 
gtmseg.mgz --no-rescale --save-input --i $PET_DIR/MeanPET.nii --reg 
$PET_DIR/reg.pet2t1.lta --psf 6 --o $PET_DIR/pvc.psf06 --default-seg-merge
sysname  Linux
hostname weckl.nmr.mgh.harvard.edu
machine  x86_64
user makaretz
vgthresh   0.001000
nReplace   18
0. 0. 0. 0. 0. 0.
Loading seg for gtm $SUBJECTS_DIR/$s/mri/gtmseg.mgz
Loading ctab $SUBJECTS_DIR/$s/mri/gtmseg.ctab
Reading $SUBJECTS_DIR/$s/mri/gtmseg.lta
Failed tissue type check
[weckl:FDG_2017-11-15] (nmr-stable6-env)

I tried re-running mri_gtmseg and adding --keep-cc, as recommended in this 
thread (I left out --no-xcerseg since I think it's now the default): 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-January/043523.html 
But I got a different error, where it's trying to write to a file called (null):
[weckl:FDG_2017-11-15] (nmr-stable6-env) mri_gtmseg --s $s --keep-cc
$Id: mri_gtmseg.c,v 1.9.2.1 2016/08/02 21:07:49 greve Exp $
cwd $PET_DIR
cmdline mri_gtmseg --s $s--keep-cc
sysname  Linux
hostname weckl.nmr.mgh.harvard.edu
machine  x86_64
user makaretz
subject $s
USF 2
OutputUSF 2
apasfile apas+head.mgz
wmannotfile NULL
ctxannotfile aparc.annot
ctxlhbase 1000
ctxrhbase 2000
SubSegWM   0
KeepHypo   0
KeepCC   1
dmax 5.00
nlist   0
lhmin  1000
lhmax  1900
rhmin  2000
rhmax  2900
Starting MRIgtmSeg()
Starting MRIgtmSeg() USF=2
Loading $SUBJECTS_DIR/$s/mri/apas+head.mgz
Loading surfaces  t = 2.1280
Loading annotations  t = 6.2390
Not segmenting WM
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
 Relabeling any unlateralized hypointenities as lateralized hypointenities
  MRIrelabelHypoHemi(): looping over volume
 nthreads = 1
 Relabeling any hypointensities as WM
  MRIunsegmentWM(): looping over volume
 nthreads = 1
Upsampling segmentation USF = 2 t = 32.3010
  MRIhiresSeg(): filling unknowns with 257
Beginning cortical segmentation using aparc.annot t = 83.9890
  MRIannot2CorticalSeg(): looping over volume
 nthreads = 1
  MRIannot2CorticalSeg(): found 1517 unknown, filled with 257
Not subsegmenting WM
Found 115 segs in the final list
MRIgtmSeg() done, t = 358.8340
Computing colortable
WARNING: segid   29 Left-undetermined tissue type is not set
Writing output file to $SUBJECTS_DIR/$s/mri/(null)
unknown file type for file ($SUBJECTS_DIR/$s/mri/(null))
[weckl:FDG_2017-11-15] (nmr-stable6-env)

I think I ruled out the usual operator errors (typos/SUBJECTS_DIR/permissions). 
Do you have any advice?

Thank you in advance for any help!
Sara
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Re: [Freesurfer] Cortical Parcellation Yeo2011

[Makaretz, Sara Johanna]

Hi Lorenzo,

I was trying to do this too, and used:

1. mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi $h
--sval-annot $h.yeo.annot
--tval $SUBJECTS_DIR/$s/label/$h.yeo.annot

2. make yeo.gtmseg.ctab - I copied gtmseg.ctab, pasted yeo network ctab at end 
(offset LH by 1000, offset RH by 2000) and added column with tissue type 
(1=cortex)
ie.1001lh_17Networks_1 120  18 134   1

3. gtmseg --s $s --o yeo.gtmseg.mgz
--ctx-annot yeo.annot 1000 2000
--ctab yeo.gtmseg.ctab

4. mri_gtmpvc --i pet.nii.gz --reg template.reg.lta
--psf FWHM --default-seg-merge
--auto-mask PSF .01 --mgx .01
--seg yeo.gtmseg.mgz
--o yeo.gtmpvc.output

This worked for me, but Doug and others can tell you if this should be done 
differently.

Best,
Sara


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lorenzo Pini 
[pini.loren...@gmail.com]
Sent: Wednesday, September 06, 2017 10:07
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Cortical Parcellation Yeo2011

Hi list,

I have already run by recon-all -all all my subjects in order to run PetSurfer. 
Output stats is saved in gtm.stats.dat and values correspond to 
Desikan-Killiany Atlas, However, I am interested in calculating values using 
Yeo atlas of 7 networks.

Do you have any suggestions to get Partial Volume Corrected values from Yeo 
atlas for each subject?
Do I have to switch to Yao atlas during recon-all -all process or during gtmseg?

Thank you
Lorenzo


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Re: [Freesurfer] Difference between -autorecon2-wm and -autorecon2-noaseg ?

[Makaretz, Sara Johanna]

Still wondering about this - thanks in advance for any help!



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Makaretz, Sara Johanna 
[smakar...@mgh.harvard.edu]
Sent: Thursday, June 01, 2017 21:30
To: Freesurfer support list
Subject: Re: [Freesurfer] Difference between -autorecon2-wm and 
-autorecon2-noaseg ?

Adding to this question, I'm wondering whether it's appropriate to do both wm & 
aseg.presurf edits at the same time, and (if yes) whether there is a difference 
between reprocessing the recon with -autorecon2-noaseg or -autorecon2-wm

ie.
Hypothetically, a subject with big ventricles is processed in FS v6.0 stable 
with the flag -bigventricles. The initial recon has wm surfs that dip into the 
posterior horn of the lateral ventricle.

1st edits: fill ventricle on wm.mgz (and other wm edits in other regions); 
reprocess w -autorecon2-wm -autorecon3
wm surfs around posterior horn of ventricle not corrected

2nd edits: in aseg.presurf.mgz, relabel problem voxels from cortex -> wm; if 
just these edits, reprocess w -autorecon2-noaseg -autorecon3

But if the subject has wm.mgz errors in other regions, can those edits be be 
made together? And would it matter whether the recon is reprocessed with 
-autorecon2-wm or -autorecon2-noaseg?

Thanks for any advice!



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Makaretz, Sara Johanna 
[smakar...@mgh.harvard.edu]
Sent: Tuesday, May 23, 2017 14:31
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Difference between -autorecon2-wm and -autorecon2-noaseg ?

Hi,

I'm using FS v6.0 stable. Is there any difference between running recon-all 
with -autorecon2-wm or -autorecon-noaseg? It looks like both are starting at 
-normalization2 and running through the rest of autorecon2 with no changes to 
inputs/args compared to "regular" -autorecon2.

Is this true, and can I use -autorecon2-wm and -autorecon2-noaseg 
interchangeably?

https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0

Thanks!
Sara
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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[Freesurfer] Difference between -autorecon2-wm and -autorecon2-noaseg ?

[Makaretz, Sara Johanna]

Hi,

I'm using FS v6.0 stable. Is there any difference between running recon-all 
with -autorecon2-wm or -autorecon-noaseg? It looks like both are starting at 
-normalization2 and running through the rest of autorecon2 with no changes to 
inputs/args compared to "regular" -autorecon2.

Is this true, and can I use -autorecon2-wm and -autorecon2-noaseg 
interchangeably?

https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0

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

Re: [Freesurfer] mris_preproc - srcsubjreg

[Makaretz, Sara Johanna]

Thank you! Does this mean that an older glm would have still used fsaverage for 
the "common surf" but then the output is mapped to the target? Outputs from 
older glms load no problem on the targets, and look "as expected"

Aka would you expect a major difference in glmfit outputs with old mris_preproc 
reg vs new mris_preproc reg?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, May 31, 2016 12:47
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc - srcsubjreg

Sorry for the delay. This is because sphere.reg only applies to
fsaverage. Previously, the specification of a different target would
only influence smoothing done as part of mris_preproc; the registration
would still be done to fsaverage. This is probably not the intent of
people who are specifying a target, so I changed mris_preproc to require
a targets-specific registration. You can generate this with

surfreg --s subject --t target

then run mris_preproc specifying the given target
doug


On 05/24/2016 04:23 PM, Makaretz, Sara Johanna wrote:
> Hi Doug, I¹m curious why the newer mris_preproc does not use sphere.reg as
> the default srcsurfreg when the target is not fsaverage - see below
>
> Thanks for any info! (not urgent)
>
>
> On 2016-5-24, 11:30, "Z K" <zkauf...@nmr.mgh.harvard.edu> wrote:
>
>> Good question, and I dont know the answer. mris_preproc is Dougs baby so
>> I suggest just posting this question to the list with "mris_preproc" in
>> the subject, and I bet he will give you the answer.
>>
>> -Zeke
>>
>> On 05/23/2016 10:31 PM, Makaretz, Sara Johanna wrote:
>>> Hi Zeke,
>>>
>>> I am running some surface glms where targ is a patient surface. The help
>>> says --target TargetSubject (requires ?h.TargetSubject.sphere.reg), and
>>> I was getting errors because dev-default mris_preproc wanted
>>> mri_surf2surf to have srcsurfreg =
>>> $SUBJECTS_DIR/$srcsubject/surf/$h.$TARGSUBJ.sphere.reg
>>>
>>> But mris_preproc in 5.3 let me do target = patient surface with no extra
>>> surf reg files or extra flags to get mri_surf2surf to use srcsurfreg =
>>> $SUBJECTS_DIR/$srcsubject/surf/$h.sphere.reg
>>>
>>> I had been running this with 5.3:
>>> mris_preproc\
>>>   --target $TARGSUBJ\
>>>   --hemi lh\
>>>   --meas thickness\
>>>   --fsgd file.fsgd\
>>>   --out lh.output.mgh
>>>
>>> And I was about to email freesurfer@nmr but "for fun" tried adding
>>> --surfreg sphere.reg which got mris_surf2surf to use the right reg
>>> files. So now I'm selfishly trying to figure this out - do you know what
>>> prompted the switch from sphere.reg "opt-out" to sphere.reg "opt-in"?
>>> Aka why sphere.reg is non-default when the target is non-fsaverage? Did
>>> that make sense? I know there must be some reason, so I really want to
>>> know a bit more so I can stay sane when old scripts break.
>>>
>>> Thanks for any info! Sorry to bother you!
>>> Sara
>>>
>>>
>>>
>>>
>>>
>>>
>>> Outputs from the FS-dev one:
>>>
>>> $Id: mris_preproc,v 1.76 2015/12/09 20:02:53 zkaufman Exp $
>>> 
>>> Src lh $TARGSUBJ.sphere.reg
>>> Trg lh sphere.reg
>>> 
>>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg
>>> $TARGSUBJ.sphere.reg --trgsubject $TARGSUBJ --trghemi lh --trgsurfreg
>>> sphere.reg --etcetcetc
>>> 
>>> ERROR can't find $SUBJECTS_DIR/$SRCSUBJ/surf/$TARGSUBJ.sphere.reg
>>> because I never made it
>>>
>>>
>>>
>>> Outputs from the FS-dev one with fsaverage as the targ subj:
>>>
>>> $Id: mris_preproc,v 1.76 2015/12/09 20:02:53 zkaufman Exp $
>>> 
>>> Src lh sphere.reg
>>> Trg lh sphere.reg
>>> 
>>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg sphere.reg
>>> --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --etcetcetc
>>> 
>>> mris_preproc finds everything, runs no problem
>>>
>>>
>>>
>>> Outputs from the FS-5.3 one:
>>>
>>> $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $
>>> 
>>> Src lh sphere.reg
>>> Trg lh sphere.reg
>>> 
>>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurf

Re: [Freesurfer] mris_preproc - srcsubjreg

[Makaretz, Sara Johanna]

Hi Doug, still wondering about this - thanks!


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Makaretz, Sara Johanna 
[smakar...@mgh.harvard.edu]
Sent: Tuesday, May 24, 2016 16:23
To: Freesurfer support list
Subject: [Freesurfer] mris_preproc - srcsubjreg

Hi Doug, I¹m curious why the newer mris_preproc does not use sphere.reg as
the default srcsurfreg when the target is not fsaverage - see below

Thanks for any info! (not urgent)


On 2016-5-24, 11:30, "Z K" <zkauf...@nmr.mgh.harvard.edu> wrote:

>Good question, and I dont know the answer. mris_preproc is Dougs baby so
>I suggest just posting this question to the list with "mris_preproc" in
>the subject, and I bet he will give you the answer.
>
>-Zeke
>
>On 05/23/2016 10:31 PM, Makaretz, Sara Johanna wrote:
>> Hi Zeke,
>>
>> I am running some surface glms where targ is a patient surface. The help
>> says --target TargetSubject (requires ?h.TargetSubject.sphere.reg), and
>> I was getting errors because dev-default mris_preproc wanted
>> mri_surf2surf to have srcsurfreg =
>> $SUBJECTS_DIR/$srcsubject/surf/$h.$TARGSUBJ.sphere.reg
>>
>> But mris_preproc in 5.3 let me do target = patient surface with no extra
>> surf reg files or extra flags to get mri_surf2surf to use srcsurfreg =
>> $SUBJECTS_DIR/$srcsubject/surf/$h.sphere.reg
>>
>> I had been running this with 5.3:
>> mris_preproc\
>>  --target $TARGSUBJ\
>>  --hemi lh\
>>  --meas thickness\
>>  --fsgd file.fsgd\
>>  --out lh.output.mgh
>>
>> And I was about to email freesurfer@nmr but "for fun" tried adding
>> --surfreg sphere.reg which got mris_surf2surf to use the right reg
>> files. So now I'm selfishly trying to figure this out - do you know what
>> prompted the switch from sphere.reg "opt-out" to sphere.reg "opt-in"?
>> Aka why sphere.reg is non-default when the target is non-fsaverage? Did
>> that make sense? I know there must be some reason, so I really want to
>> know a bit more so I can stay sane when old scripts break.
>>
>> Thanks for any info! Sorry to bother you!
>> Sara
>>
>>
>>
>>
>>
>>
>> Outputs from the FS-dev one:
>>
>> $Id: mris_preproc,v 1.76 2015/12/09 20:02:53 zkaufman Exp $
>> 
>> Src lh $TARGSUBJ.sphere.reg
>> Trg lh sphere.reg
>> 
>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg
>> $TARGSUBJ.sphere.reg --trgsubject $TARGSUBJ --trghemi lh --trgsurfreg
>> sphere.reg --etcetcetc
>> 
>> ERROR can't find $SUBJECTS_DIR/$SRCSUBJ/surf/$TARGSUBJ.sphere.reg
>> because I never made it
>>
>>
>>
>> Outputs from the FS-dev one with fsaverage as the targ subj:
>>
>> $Id: mris_preproc,v 1.76 2015/12/09 20:02:53 zkaufman Exp $
>> 
>> Src lh sphere.reg
>> Trg lh sphere.reg
>> 
>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg sphere.reg
>> --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --etcetcetc
>> 
>> mris_preproc finds everything, runs no problem
>>
>>
>>
>> Outputs from the FS-5.3 one:
>>
>> $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $
>> 
>> Src lh sphere.reg
>> Trg lh sphere.reg
>> 
>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg sphere.reg
>> --trgsubject $TARGSUBJ --trghemi lh --trgsurfreg sphere.reg --etcetcetc
>> 
>> mris_preproc exits with no errors because everything exists
>>
>>
>>
>>


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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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[Freesurfer] mris_preproc - srcsubjreg

[Makaretz, Sara Johanna]

Hi Doug, I¹m curious why the newer mris_preproc does not use sphere.reg as
the default srcsurfreg when the target is not fsaverage - see below

Thanks for any info! (not urgent)


On 2016-5-24, 11:30, "Z K" <zkauf...@nmr.mgh.harvard.edu> wrote:

>Good question, and I dont know the answer. mris_preproc is Dougs baby so
>I suggest just posting this question to the list with "mris_preproc" in
>the subject, and I bet he will give you the answer.
>
>-Zeke
>
>On 05/23/2016 10:31 PM, Makaretz, Sara Johanna wrote:
>> Hi Zeke,
>>
>> I am running some surface glms where targ is a patient surface. The help
>> says --target TargetSubject (requires ?h.TargetSubject.sphere.reg), and
>> I was getting errors because dev-default mris_preproc wanted
>> mri_surf2surf to have srcsurfreg =
>> $SUBJECTS_DIR/$srcsubject/surf/$h.$TARGSUBJ.sphere.reg
>>
>> But mris_preproc in 5.3 let me do target = patient surface with no extra
>> surf reg files or extra flags to get mri_surf2surf to use srcsurfreg =
>> $SUBJECTS_DIR/$srcsubject/surf/$h.sphere.reg
>>
>> I had been running this with 5.3:
>> mris_preproc\
>>  --target $TARGSUBJ\
>>  --hemi lh\
>>  --meas thickness\
>>  --fsgd file.fsgd\
>>  --out lh.output.mgh
>>
>> And I was about to email freesurfer@nmr but "for fun" tried adding
>> --surfreg sphere.reg which got mris_surf2surf to use the right reg
>> files. So now I'm selfishly trying to figure this out - do you know what
>> prompted the switch from sphere.reg "opt-out" to sphere.reg "opt-in"?
>> Aka why sphere.reg is non-default when the target is non-fsaverage? Did
>> that make sense? I know there must be some reason, so I really want to
>> know a bit more so I can stay sane when old scripts break.
>>
>> Thanks for any info! Sorry to bother you!
>> Sara
>>
>>
>>
>>
>>
>>
>> Outputs from the FS-dev one:
>>
>> $Id: mris_preproc,v 1.76 2015/12/09 20:02:53 zkaufman Exp $
>> 
>> Src lh $TARGSUBJ.sphere.reg
>> Trg lh sphere.reg
>> 
>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg
>> $TARGSUBJ.sphere.reg --trgsubject $TARGSUBJ --trghemi lh --trgsurfreg
>> sphere.reg --etcetcetc
>> 
>> ERROR can't find $SUBJECTS_DIR/$SRCSUBJ/surf/$TARGSUBJ.sphere.reg
>> because I never made it
>>
>>
>>
>> Outputs from the FS-dev one with fsaverage as the targ subj:
>>
>> $Id: mris_preproc,v 1.76 2015/12/09 20:02:53 zkaufman Exp $
>> 
>> Src lh sphere.reg
>> Trg lh sphere.reg
>> 
>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg sphere.reg
>> --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --etcetcetc
>> 
>> mris_preproc finds everything, runs no problem
>>
>>
>>
>> Outputs from the FS-5.3 one:
>>
>> $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $
>> 
>> Src lh sphere.reg
>> Trg lh sphere.reg
>> 
>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg sphere.reg
>> --trgsubject $TARGSUBJ --trghemi lh --trgsurfreg sphere.reg --etcetcetc
>> 
>> mris_preproc exits with no errors because everything exists
>>
>>
>>
>>


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Re: [Freesurfer] Map label from lh to rh

[Makaretz, Sara Johanna]

Thanks Doug that worked great!


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, March 01, 2016 15:33
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Map label from lh to rh

It does not. You can run  mris_left_right_register. You will need to use
mris_apply_reg instead of mri_label2label. See below. run with --help to
get docs

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg

On 02/25/2016 04:28 PM, Makaretz, Sara Johanna wrote:
> Hi, I want to map a label from one hemi to the other (all on
> fsaverage). I tried mri_label2label:
>
> mri_label2label --s fsaverage --srchemi lh --trghemi rh --srclabel
> lh.a.label --trglabel rh.flipped_lh.a.label --regmethod surface
>
> but I think I need to specify a reg file to go between hemispheres,
> does this exist somewhere? an error message kindly pointed out that
> this one does not exist:
> /usr/local/freesurfer/stable5_3_0/subjects/fsaverage/surf/rh.lh.sphere.reg
>
>
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> Freesurfer@nmr.mgh.harvard.edu
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] AAL atlas question

[Makaretz, Sara Johanna]

I'm actually wondering the same thing re AAL to subject space - this is what I 
have been using:

spmregister - reg template to subject
mri_label2vol - move AAL to subject space
mri_segstats - pull in-volume stats using AAL in subject space
mri_vol2surf - project AAL (subject space) to subject surface
mris_anatomical stats - pull surface stats

Am I making that more complicated than it needs to be? What I'm most unsure 
about is whether the atlas should be projected to the template surface then 
moved to subject surface, or if it should be moved to subject space then 
projected to surface.

Thanks!
Sara


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of 
pfot...@nmr.mgh.harvard.edu [pfot...@nmr.mgh.harvard.edu]
Sent: Monday, February 29, 2016 18:37
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] AAL atlas question

Hi FS community,

I have recon-ed a set of subjects and I was interested in also obtaining
structural info (cortical thickness, gray matter volume, surface area
etc.) based on a different atlas than the ones FS is using, and in
particular the AAL atlas.

I was wondering whether my approach would be the correct one or whether
there is another (better and more accurate) approach:

1) Convert the AAL atlas into a surface (with mri_vol2surf) from the MNI
space into the native subjects' space,
2) Use mris_anatomical_stats to calculate the structural stats

Sorry for the potentially trivial question, and thank you for your time!

Best,
Panos

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[Freesurfer] Map label from lh to rh

[Makaretz, Sara Johanna]

Hi, I want to map a label from one hemi to the other (all on fsaverage). I 
tried mri_label2label:

mri_label2label --s fsaverage --srchemi lh --trghemi rh --srclabel lh.a.label 
--trglabel rh.flipped_lh.a.label --regmethod surface

but I think I need to specify a reg file to go between hemispheres, does this 
exist somewhere? an error message kindly pointed out that this one does not 
exist: 
/usr/local/freesurfer/stable5_3_0/subjects/fsaverage/surf/rh.lh.sphere.reg
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[Freesurfer] mri_label2vol - output volume appears cut off

[Makaretz, Sara Johanna]

Hi all, I am having a problem with moving aparc+aseg to different dimensions. I 
have successfully resliced aparc+asegs for several other subjects, but the 
resliced volume for one subject appears cut-off at the bottom. The dimensions 
match for this subject's template and output volumes, and the original 
aparc+aseg looks fine. This is what I have been running for all of the subjects:

mri_label2vol --subject ${s} --seg ${s}/mri/aparc+aseg.mgz --temp 
${s}/template_vol.nii --regheader ${s}/mri/T1.mgz --fillthresh .3 --o 
${s}/rs_aparc+aseg.nii

Thank you for any tips!

Sara
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[Freesurfer] Aparc stats with different input

[Makaretz, Sara Johanna]

Hi,
I have a PET volume that is registered to a recon, then projected to the 
surface via vol2surf. I would like to pull stats for the PET using aparc 
regions. Should I use mri_annotation2label, then pull stats for each label? Or 
is there something similar to mri_segstats, ie. --annot lh.aparc.annot --in 
pet_surf.mgz --ctab-default --sum stats.table ?
Thank you for your help!
Sara
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[Freesurfer] Reconstruct tm3d warp from mri_cvs_register

[Makaretz, Sara Johanna]

Hi all,

I ran mri_cvs_register but forgot to add --nocleanup. I have the final
combined m3z and no tm3d, and for el_reg just mgz files. Can I recreate
the tm3d combined with just these files?

On the wiki it says use createMorph - I tried different inputs in 5.3
and dev environments with no success.
(https://surfer.nmr.mgh.harvard.edu/fswiki/mri_cvs_register)

Thanks,
Sara

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Re: [Freesurfer] mri_em_register intervention?

[Makaretz, Sara Johanna]

Hi Bruce and others,

Thanks for the reply! I cloned in all of the brain to the brainmask and ran 
-autorecon2. What I have so far looks a lot better, but -autorecon2 exited with 
errors. In recon-all.log it looks like mris_curvature_stats went fine, then it 
says INFO: mri_segstats will not calculate Supratentorial due to missing 
ribbon.mgz file

I thought ribbon.mgz would be created in -autorecon3. Is it okay to just run 
-autorecon3 now, or should I fix something first?

Thank you!
Sara





On 08/11/2014 11:54 AM, Bruce Fischl wrote:
 It looks more likely that it is a problem with the skull stripping. If you 
 clone the brain voxels back in and rerun do things work?

 On Aug 11, 2014, at 4:11 PM, Makaretz, Sara Johanna 
 smakar...@mgh.harvard.edu wrote:

 I am having trouble getting a usable brainmask for one of my subjects -
 a screenshot of the initial brainmask.mgz is attached as image_1. The
 talairach transformation looks fine, so I tried running recon-all
 -multistrip with raised watershed heights to no avail - see image_2.

 Does this mean the problem is with the mri_em_register step / lta
 output? How can I check this, and what can I try changing?

 Thank you!
 image_1.jpg
 image_2.jpg
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[Freesurfer] Updated process v. files excel sheet?

[Makaretz, Sara Johanna]

Hi all,

I like the excel presentation of the recon-all process/files table for 
Freesurfer 3.0.5 found here: 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllFilesVsSteps
Is there an updated document for a more recent version? (I am using 5.3.0)

Also, are 5.2 and 5.3 similar enough to reference the 5.2 stable table for file 
order/rerunning steps? 
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.2)

Thank you!

Sara


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