[Freesurfer] PETSurfer voxelwise statistic

[Boris Rauchmann]

External Email - Use Caution

Dear all,

How can I run a voxelwise statistic using grey and white matter uptake?
mgx.ctxgm.nii.gz and the other files in output all only include gm as I
understand.

My goal is to run whole brain volume-based analysis. Like in this example
for subcortical analysis:

mri_vol2vol --mov subctxgm.nii.gz --reg aux/bbpet2anat.lta
--tal --talres 2  --o subctxgm.mni305.2mm.sm00.nii.gz


Thanks,
Boris
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[Freesurfer] PETSurfer

[Boris Rauchmann]

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Dear all,

How can I easily scale the mgx.ctxgm.nii.gz files with the whole brain mean
intensity using PETSufer? Is there a command to use in mri_gtmpvc like
--rescale X?
I know that I can find the mean in  global.gm.dat and I can use that value
for scaling the atlas based results in gtm.stats.dat but how can I easily
scale the image?

Thanks,
Boris
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[Freesurfer] tkregisterfv -ss

[Boris Rauchmann]

External Email - Use Caution

Dear all,

is there a way to use  freeviews -ss command to obtain snapshots
using tkregisterfv? I have a bunch of registrations to check and would
prefer to do that using a bash script and snapshots.

tkregisterfv --mov template.nii.gz --reg template.reg.lta --surfs -ss

Gives back ERROR: Flag -ss unrecognized.

Thanks,
Boris
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Re: [Freesurfer] gtmseg getSignalBehindHead ERROR (no slices behind head)

[Boris Rauchmann]

External Email - Use Caution

thanks, the subj I sent you the logfile has a cut on the posterior part, I
uploaded a similar case 098_S_4275_20181221.tar.gz
Is there any way to run gtmseg regardless?

Thanks

Am Fr., 5. Juni 2020 um 20:01 Uhr schrieb Douglas N. Greve <
dgr...@mgh.harvard.edu>:

> Hmmm, not sure what is going on here. I'm guessing that the back of the
> head was cut off (or wrapped around). Is that right? I'm not sure why this
> would create an error. If you upload one of your subjects, I'll take a
> look. See instructions below
>
> 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 6/4/2020 9:40 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
> Please find the logfile attached.
>
> Thank you
>
> Am Do., 4. Juni 2020 um 15:18 Uhr schrieb Douglas N. Greve <
> dgr...@mgh.harvard.edu>:
>
>> Can you send the log file?
>>
>> On 6/4/2020 9:12 AM, Boris Rauchmann wrote:
>>
>> External Email - Use Caution
>> Dear FS experts,
>>
>> In my dataset I have 4 subjects where the T1 was acquired, planning the
>> FOV very close to the occipital lobe. I guess that triggers the error:
>> getSignalBehindHead ERROR (no slices behind head) WARNING: only 0 < 7
>> slices behind head! ERROR: xcerebralseg  and results in gtmseg exited with
>> errors.
>> How can I fix this?
>>
>> Best regards,
>> Boris
>>
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>>
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>
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Re: [Freesurfer] gtmseg getSignalBehindHead ERROR (no slices behind head)

[Boris Rauchmann]

External Email - Use Caution

Please find the logfile attached.

Thank you

Am Do., 4. Juni 2020 um 15:18 Uhr schrieb Douglas N. Greve <
dgr...@mgh.harvard.edu>:

> Can you send the log file?
>
> On 6/4/2020 9:12 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
> Dear FS experts,
>
> In my dataset I have 4 subjects where the T1 was acquired, planning the
> FOV very close to the occipital lobe. I guess that triggers the error:
> getSignalBehindHead ERROR (no slices behind head) WARNING: only 0 < 7
> slices behind head! ERROR: xcerebralseg  and results in gtmseg exited with
> errors.
> How can I fix this?
>
> Best regards,
> Boris
>
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Log file for gtmseg
Thu Jun  4 14:40:20 CEST 2020

setenv SUBJECTS_DIR /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS
cd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS
/usr/local/freesurfer/bin/gtmseg --s 098_S_6655_20190107

freesurfer-linux-centos6_x86_64-dev-20180911-69aa645
$Id: gtmseg,v 1.19 2016/03/24 17:32:23 greve Exp $
Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18 09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
xcerebralseg --s 098_S_6655_20190107
Thu Jun  4 14:40:20 CEST 2020

setenv SUBJECTS_DIR /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS
cd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS
/usr/local/freesurfer/bin/xcerebralseg --s 098_S_6655_20190107

freesurfer-linux-centos6_x86_64-dev-20180911-69aa645
$Id: xcerebralseg,v 1.12 2017/01/18 21:21:00 zkaufman Exp $
Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18 09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
mri_ca_label -align -nobigventricles /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/nu.mgz /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/transforms/talairach.m3z /usr/local/freesurfer/average/aseg+spmhead+vermis+pons.ixi.gca /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.mgh
sysname  Linux
hostname linuxrechner2
machine  x86_64

setenv SUBJECTS_DIR /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS
cd /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS
mri_ca_label -align -nobigventricles /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/nu.mgz /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/transforms/talairach.m3z /usr/local/freesurfer/average/aseg+spmhead+vermis+pons.ixi.gca /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/tmp/tmpdir.xcerebralseg.31646/seg1.mgh 


== Number of threads available to mri_ca_label for OpenMP = 1 == 
renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-renormalize_mean 0.500
	-regularize 0.500
not handling expanded ventricles...
reading 1 input volumes
reading classifier array from /usr/local/freesurfer/average/aseg+spmhead+vermis+pons.ixi.gca
reading input volume from /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/nu.mgz
average std[0] = 20.4
reading transform from /media/demenzbild/Studiendaten4/MS4A6A_rs610923_project/new_data/T1/WHOLE_FS_DATASET_180TauPET_FS/098_S_6655_20190107/mri/transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 7.01
Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca
average std = 20.4   using min determinant for regularization = 41.8
0 singular and 0 ill-conditioned covariance matrices regularized
labeling volume...
renormalizing by structure alignment
renormalizing input #0
gca peak = 0.24861 (36)
mri peak = 0.08632 (27)
Left_Lateral_Ventricle (4): linear fit = 0.69 x + 0.0 (14329 voxels, overlap=0.008)
Left_Lateral_Ventricle (4): linear fit = 0.69 x + 0.0 (14329 voxels, peak = 25), gca=25.0
gca peak = 0.29857 (37)
mri peak = 0.08013 (27)
Right_Lateral_Ventricle (43): linear fit = 0.64 x + 0.0 (12114 voxels, overlap=

[Freesurfer] gtmseg getSignalBehindHead ERROR (no slices behind head)

[Boris Rauchmann]

External Email - Use Caution

Dear FS experts,

In my dataset I have 4 subjects where the T1 was acquired, planning the FOV
very close to the occipital lobe. I guess that triggers the error:
getSignalBehindHead ERROR (no slices behind head) WARNING: only 0 < 7
slices behind head! ERROR: xcerebralseg  and results in gtmseg exited with
errors.
How can I fix this?

Best regards,
Boris
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Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Thanks, that solution seems to work finally. I just ignored the remaining 
voxels labeled according to the standard aseg scheme and proceeded with the the 
PET analysis and the combined LUT.
I will ignore the remaining fragment labels from the original aseg and only use 
the output from the BN labels (starting with 211), these are the only results 
im really interested in. Is that ok?

Here an example stats file I got:

  12 Left-Cerebral-White-Matter  wm 41550 13909.534
0.989   0.0935
  27 Left-Cerebellum-White-Matterwm  2276 1037.525
0.854   0.0811
  38 Left-Cerebellum-Cortex  cortex 10936 6010.637
1.015   0.1339
  4   10 Left-Thalamus-Propersubcort_gm 30.024   
-0.815   0.2251
  5   11 Left-Caudatesubcort_gm 30.035   
21.480   0.1746
  6   12 Left-Putamensubcort_gm250.459
3.161   0.0615
  7   13 Left-Pallidum   subcort_gm491.497
1.474   0.0667
  8   16 Brain-Stem  subcort_gm  4599 2714.856
0.929   0.1000
  9   17 Left-Hippocampussubcort_gm 20.023   
-3.152   0.1702
 10   18 Left-Amygdala   subcort_gm 10.005   
-7.082   0.1060
 11   24 CSF csf 7468 2623.527
0.251   0.2568
 12   26 Left-Accumbens-area subcort_gm 00.004
0.879  nan
 13   28 Left-VentralDC  subcort_gm   714  205.288
1.358   0.1427
 14   31 Left-choroid-plexus csf  220   18.333
5.945   0.6080
 15   41 Right-Cerebral-White-Matter wm 40645 13911.597
0.987   0.0841
 16   46 Right-Cerebellum-White-Matter   wm  2146  990.941
0.862   0.0826
 17   47 Right-Cerebellum-Cortex cortex 11029 6187.241
0.985   0.1317
 18   49 Right-Thalamus-Proper   subcort_gm110.140
0.032   0.2024
 19   50 Right-Caudate   subcort_gm 10.009   
-2.162   0.0258
 20   51 Right-Putamen   subcort_gm442.020
3.727   0.1893
 21   52 Right-Pallidum  subcort_gm240.316
5.739   0.1814
 22   53 Right-Hippocampus   subcort_gm 30.026   
16.575   0.2951
 23   54 Right-Amygdala  subcort_gm 70.081
4.637   0.0897
 24   58 Right-Accumbens-areasubcort_gm 00.000   
-4.474  nan
 25   60 Right-VentralDC subcort_gm   728  198.051
1.430   0.2142
 26   63 Right-choroid-plexuscsf  136   10.088
6.633   0.5924
 27  211 mAmyg_L subcort_gm   264   48.960
1.126   0.1262
 28  212 mAmyg_R subcort_gm   268   46.429
1.292   0.1920
 29  213 lAmyg_L subcort_gm   1316.503
1.889   0.1003
 30  214 lAmyg_R subcort_gm   181   13.490
1.382   0.1237
 31  215 rHipp_L subcort_gm  1020  260.090
1.166   0.1828
 32  216 rHipp_R subcort_gm   833  241.777
1.149   0.2291
 33  217 cHipp_L subcort_gm   911  288.346
1.578   0.3201
 34  218 cHipp_R subcort_gm  1050  330.445
1.273   0.2312
 35  219 vCa_L   subcort_gm   626  170.254
1.205   0.0829
 36  220 vCa_R   subcort_gm   477   84.269
1.491   0.0933
 37  221 GP_Lsubcort_gm   597  133.161
1.369   0.0977
 38  222 GP_Rsubcort_gm   514   93.978
1.491   0.0811
 39  223 NAC_L   subcort_gm   412   67.647
1.348   0.1591
 40  224 NAC_R   subcort_gm   503   87.917
1.240   0.1258
 41  225 vmPu_L  subcort_gm   465  128.509
1.740   0.0783
 42  226 vmPu_R  subcort_gm   367   83.411
1.588   0.0699
 43  227 dCa_L   subcort_gm   997  255.259
0.821   0.1448
 44  228 dCa_R   subcort_gm  1271  405.156
1.017   0.1380
 45  229 dlPu_L  subcort_gm   678  122.256
1.356   0.0960
 46  230 dlPu_R  subcort_gm   585  150.878
1.319   0.0942
 47  231 mPFtha_L  

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Ok. i figured it out. The problem was just that you can not specify the
file type - so .mgz in  BN_Atlas_subcotex.mgz was actually the problem.

Now I run in a new issue:

gtmseg --head BN_apas+head.mgz --s 1122_test --o NEU_BN.gtmseg.mgz
--ctx-annot BN_Atlas.annot --ctab
'/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt'

Wed Jan  8 17:04:12 CET 2020

setenv SUBJECTS_DIR
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects
cd /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects
/usr/local/freesurfer/bin/gtmseg --head BN_apas+head.mgz --s 1122_test --o
NEU_BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt

freesurfer-linux-centos6_x86_64-dev-20180911-69aa645
$Id: gtmseg,v 1.19 2016/03/24 17:32:23 greve Exp $
Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18
09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas
BN_apas+head.mgz --ctx-annot BN_Atlas.annot --ctab
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt
--no-subseg-wm --no-keep-cc --no-keep-hypo

$Id: mri_gtmseg.c,v 1.10 2016/08/02 21:07:24 greve Exp $
cwd /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects
cmdline mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas
BN_apas+head.mgz --ctx-annot BN_Atlas.annot --ctab
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt
--no-subseg-wm --no-keep-cc --no-keep-hypo
sysname  Linux
hostname linuxrechner2
machine  x86_64
user demenzbild
subject 1122_test
USF 2
OutputUSF 2
apasfile BN_apas+head.mgz
wmannotfile NULL
ctxannotfile BN_Atlas.annot
ctxlhbase 1000
ctxrhbase 2000
SubSegWM   0
KeepHypo   0
KeepCC   0
dmax 5.00
nlist   0
lhmin  1000
lhmax  1900
rhmin  2000
rhmax  2900
mri_gtmseg supposed to be reproducible but seed not set
Starting MRIgtmSeg()
Starting MRIgtmSeg() USF=2
Loading
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/1122_test/mri/BN_apas+head.mgz
Loading surfaces  t = 2.1510
Loading annotations  t = 4.8510
Not segmenting WM
reading colortable from annotation file...
colortable with 211 entries read (originally ./BN_Atlas_210_LUT.txt)
reading colortable from annotation file...
colortable with 211 entries read (originally ./BN_Atlas_210_LUT.txt)
 Relabeling any unlateralized hypointenities as lateralized hypointenities
  MRIrelabelHypoHemi(): looping over volume
 nthreads = 1
 Relabeling CC as WM
 Relabeling any hypointensities as WM
  MRIunsegmentWM(): looping over volume
 nthreads = 1
Upsampling segmentation USF = 2 t = 7.3520
  MRIhiresSeg(): filling unknowns with 257
Beginning cortical segmentation using BN_Atlas.annot t = 41.3800
  MRIannot2CorticalSeg(): looping over volume
 nthreads = 1
  MRIannot2CorticalSeg(): found 2347 unknown, filled with 257
Not subsegmenting WM
Found 279 segs in the final list
MRIgtmSeg() done, t = 224.1820
Computing colortable
ERROR: cannot find match for subcortical segid 227
ERROR: mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas
BN_apas+head.mgz --ctx-annot BN_Atlas.annot --ctab
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt
--no-subseg-wm --no-keep-cc --no-keep-hypo
gtmseg exited with errors

Before I run gtmseg I used xcerebralseg --s 1122_test --m
aparc+BN_Atlas_subcotex.mgz --atlas
'/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_subcortex.gca'
 --o BN_apas+head.mgz

Any ideas on that?

Best,
Boris

Am Mo., 6. Jan. 2020 um 23:14 Uhr schrieb Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:

> Are you sure you have permission to view that file?
>
> On 1/6/20 5:01 PM, Boris Rauchmann wrote:
> >  External Email - Use Caution
> >
> > I’m sure just double checked it. I don’t know what’s wrong here.
> >
> > Von meinem iPhone gesendet
> >
> >>> Am 06.01.2020 um 18:35 schrieb Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu>:
> >> This is not making any sense to me. Are you sure you are in
> >> $SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that
> >> BN_Atlas_subcotex.mgz is in the same folder?
> >>
> >>> On 1/3/20 3:07 PM, Boris Rauchmann wrote:
> >>>
> >>>  External Email - Use Caution
> >>>
> >>> Thank you for testing it. As before I get the same error message.
> >>> Do you know what I´m doing wrong here?
> >>>
> >>> Best,
> >>> Boris
> >>>
> >>> MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg
> >>> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
> >>> SUBJECTS_DIR /Users/bori

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

I’m sure just double checked it. I don’t know what’s wrong here. 

Von meinem iPhone gesendet

>> Am 06.01.2020 um 18:35 schrieb Greve, Douglas N.,Ph.D. 
>> :
> This is not making any sense to me. Are you sure you are in 
> $SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that 
> BN_Atlas_subcotex.mgz is in the same folder?
> 
>> On 1/3/20 3:07 PM, Boris Rauchmann wrote:
>> 
>> External Email - Use Caution
>> 
>> Thank you for testing it. As before I get the same error message.
>> Do you know what I´m doing wrong here?
>> 
>> Best,
>> Boris
>> 
>> MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg 
>> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
>> SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
>> subject 1122
>> outvol aparc+BN_Atlas_subcotex.mgz
>> useribbon 0
>> baseoffset 0
>> RipUnknown 0
>> 
>> Reading lh white surface
>>  /Users/boris/Desktop/MirLIND_test/1122/surf/lh.white
>> 
>> Reading lh pial surface
>>  /Users/boris/Desktop/MirLIND_test/1122/surf/lh.pial
>> 
>> Loading lh annotations from 
>> /Users/boris/Desktop/MirLIND_test/1122/label/lh.aparc.annot
>> 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 rh white surface
>>  /Users/boris/Desktop/MirLIND_test/1122/surf/rh.white
>> 
>> Reading rh pial surface
>>  /Users/boris/Desktop/MirLIND_test/1122/surf/rh.pial
>> 
>> Loading rh annotations from 
>> /Users/boris/Desktop/MirLIND_test/1122/label/rh.aparc.annot
>> reading colortable from annotation file...
>> colortable with 36 entries read (originally 
>> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>> Have color table for lh white annotation
>> Have color table for rh white annotation
>> Loading ribbon segmentation from 
>> /Users/boris/Desktop/MirLIND_test/1122/mri/ribbon.mgz
>> 
>> Building hash of lh white
>> 
>> Building hash of lh pial
>> 
>> Building hash of rh white
>> 
>> Building hash of rh pial
>> ERROR: cannot find aseg
>> MacBook-Pro:mri boris$
>> 
>> 
>>> Am 03.01.2020 um 17:46 schrieb Greve, Douglas N.,Ph.D.
>>> mailto:dgr...@mgh.harvard.edu>>:
>>> OK, using the data you sent I was able to get mri_aparc2aseg to run.
>>> Can you try this command again?
>>> On 12/12/2019 11:57 AM, Boris Rauchmann wrote:
>>>> External Email - Use Caution
>>>> My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg
>>>> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
>>>> SUBJECTS_DIR /Users/boris/Desktop/mydir
>>>> subject 1122
>>>> outvol aparc+BN_Atlas_subcotex.mgz
>>>> useribbon 0
>>>> baseoffset 0
>>>> RipUnknown 0
>>>> Reading lh white surface
>>>>  /Users/boris/Desktop/mydir/1122/surf/lh.white
>>>> Reading lh pial surface
>>>>  /Users/boris/Desktop/mydir/1122/surf/lh.pial
>>>> Loading lh annotations from
>>>> /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot
>>>> 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 rh white surface
>>>>  /Users/boris/Desktop/mydir/1122/surf/rh.white
>>>> Reading rh pial surface
>>>>  /Users/boris/Desktop/mydir/1122/surf/rh.pial
>>>> Loading rh annotations from
>>>> /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot
>>>> reading colortable from annotation file...
>>>> colortable with 36 entries read (originally
>>>> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>>>> Have color table for lh white annotation
>>>> Have color table for rh white annotation
>>>> Loading ribbon segmentation from
>>>> /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
>>>> Building hash of lh white
>>>> Building hash of lh pial
>>>> Building hash of rh white
>>>> Building hash of rh pial
>>>> ERROR: cannot find aseg
>>>> I get the same result using aseg.mgz
>>>> Thanks,
>>>> Boris
>>>>> Am 12.12.

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Thank you for testing it. As before I get the same error message. 
Do you know what I´m doing wrong here?

Best, 
Boris

MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg 
BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
subject 1122
outvol aparc+BN_Atlas_subcotex.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /Users/boris/Desktop/MirLIND_test/1122/surf/lh.white

Reading lh pial surface 
 /Users/boris/Desktop/MirLIND_test/1122/surf/lh.pial

Loading lh annotations from 
/Users/boris/Desktop/MirLIND_test/1122/label/lh.aparc.annot
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 rh white surface 
 /Users/boris/Desktop/MirLIND_test/1122/surf/rh.white

Reading rh pial surface 
 /Users/boris/Desktop/MirLIND_test/1122/surf/rh.pial

Loading rh annotations from 
/Users/boris/Desktop/MirLIND_test/1122/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from 
/Users/boris/Desktop/MirLIND_test/1122/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial
ERROR: cannot find aseg
MacBook-Pro:mri boris$


> Am 03.01.2020 um 17:46 schrieb Greve, Douglas N.,Ph.D. 
> :
> 
> OK, using the data you sent I was able to get mri_aparc2aseg to run. Can you 
> try this command again?
> 
> On 12/12/2019 11:57 AM, Boris Rauchmann wrote:
>> External Email - Use Caution
>> 
>> My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg 
>> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
>> SUBJECTS_DIR /Users/boris/Desktop/mydir
>> subject 1122
>> outvol aparc+BN_Atlas_subcotex.mgz
>> useribbon 0
>> baseoffset 0
>> RipUnknown 0
>> 
>> Reading lh white surface 
>>  /Users/boris/Desktop/mydir/1122/surf/lh.white
>> 
>> Reading lh pial surface 
>>  /Users/boris/Desktop/mydir/1122/surf/lh.pial
>> 
>> Loading lh annotations from 
>> /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot
>> 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 rh white surface 
>>  /Users/boris/Desktop/mydir/1122/surf/rh.white
>> 
>> Reading rh pial surface 
>>  /Users/boris/Desktop/mydir/1122/surf/rh.pial
>> 
>> Loading rh annotations from 
>> /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot
>> reading colortable from annotation file...
>> colortable with 36 entries read (originally 
>> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>> Have color table for lh white annotation
>> Have color table for rh white annotation
>> Loading ribbon segmentation from 
>> /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
>> 
>> Building hash of lh white
>> 
>> Building hash of lh pial
>> 
>> Building hash of rh white
>> 
>> Building hash of rh pial
>> ERROR: cannot find aseg
>> 
>> 
>> I get the same result using aseg.mgz 
>> 
>> Thanks,
>> Boris
>>> Am 12.12.2019 um 17:37 schrieb Bruce Fischl >> <mailto:fis...@nmr.mgh.harvard.edu>>:
>>> 
>>> Hi Boris
>>> 
>>> can you send us the full command line and screen output of the commands 
>>> that are failing?
>>> 
>>> cheers
>>> Bruce
>>> On Thu, 12 Dec 2019, Boris Rauchmann wrote:
>>> 
>>>> External Email - Use Caution
>>>> Thanks. unfortunately I get an error message when I use the --aseg flag 
>>>> for BN_Atlas_subcotex.mgz but
>>>> even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg
>>>> .../fs_all_subjects/xyz/mri/aseg.mgz
>>>> The file BN_Atlas_subcotex.mgz was created using: 
>>>> mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
>>>> $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
>>>> $SUBJECTS_DIR/BN_Atlas_subcortex.gca
>>>> $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz
>>>> Best,
>>>> Boris
>>>> On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. 
>>>> mailto:dgr...@mgh.harvard.

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Dear Douglas,

I uploaded two files: 1122.tar.gz is the sample subject and 
BN_Atlas_freesurfer.tar.gz this is the Atlas I want use for the cortical and 
subcortical parcellation/segmentation.

Thank you so much,
Boris


> Am 02.01.2020 um 17:06 schrieb Greve, Douglas N.,Ph.D. 
> :
> 
> .

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Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

This is the log when I´m creating this file:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label 
$SUBJECTS_DIR/1122/mri/brain.mgz 
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z 
$SUBJECTS_DIR/BN_Atlas_subcortex.gca 
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
sysname  Darwin
hostname MacBook.local
machine  x86_64

setenv SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
cd /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer
mri_ca_label /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz 
/Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca 
/Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz 


== Number of threads available to mri_ca_label for OpenMP = 1 == 
reading 1 input volumes
reading classifier array from 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca
reading input volume from /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz
reading transform from 
/Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 4.97
Atlas used for the 3D morph was 
/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca
average std = 10.8   using min determinant for regularization = 11.7
0 singular and 129 ill-conditioned covariance matrices regularized
labeling volume...
0 gm and wm labels changed (%nan to gray, %nan to white out of all changed 
labels)
0 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 9576 changed.
pass 2: 3286 changed.
MRItoUCHAR: min=0, max=246
MRItoUCHAR: converting to UCHAR
writing labeled volume to 
/Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz
mri_ca_label utimesec146.184667
mri_ca_label stimesec1.040963
mri_ca_label ru_maxrss   1436573696
mri_ca_label ru_ixrss0
mri_ca_label ru_idrss0
mri_ca_label ru_isrss0
mri_ca_label ru_minflt   609288
mri_ca_label ru_majflt   112
mri_ca_label ru_nswap0
mri_ca_label ru_inblock  0
mri_ca_label ru_oublock  4
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw3
mri_ca_label ru_nivcsw   36417
auto-labeling took 2 minutes and 28 seconds.

This is what I get when I do mrs_info on the gas:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_info 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gca 
reading frame -1 of gca
Volume information for 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gca
  type: GCA
dimensions: 256 x 256 x 256 x 3
   voxel sizes: 1.00, 1.00, 1.00
  type: FLOAT (3)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 3
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r = 0.
  : x_a =   0., y_a =   0., z_a =   1., c_a = 0.
  : x_s =   0., y_s =  -1., z_s =   0., c_s = 0.
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.   0.   128.
0.   0.   1.  -128.
0.  -1.   0.   128.
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0.   128.
   -0.  -0.  -1.   128.
   -0.   1.  -0.   128.
   -0.  -0.  -0. 1.




> Am 16.12.2019 um 21:21 schrieb Boris Rauchmann :
> 
> Thanks, it was created using: 
> 
> mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz
> $SUBJECTS_DIR/1122/mri/transforms/talairach.m3z
> $SUBJECTS_DIR/BN_Atlas_subcortex.gca
> $SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
> 
> Best,
> Boris
> 
> 
>> Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D. 
>> mailto:dgr...@mgh.harvard.edu>>:
>> 
>> There is something weird about that file. How was it created?
>> doug
>> ps. Please include previous correspondence in the email
>> 
>> On 12/16/19 1:12 PM, Boris Rauchmann wrote:
>>> 
>>> External Email - Use Caution
>>> 
>>> Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz
>>> mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, 
>>> -1): could not open file
>>> 
>>>> Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. 
>>>> mailto:dgr...@mgh.harvard.edu> 
>>>> <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>>:
>&

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Thanks, it was created using: 

mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz

Best,
Boris


> Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D. 
> :
> 
> There is something weird about that file. How was it created?
> doug
> ps. Please include previous correspondence in the email
> 
> On 12/16/19 1:12 PM, Boris Rauchmann wrote:
>> 
>> External Email - Use Caution
>> 
>> Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz
>> mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, 
>> -1): could not open file
>> 
>>> Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. 
>>> mailto:dgr...@mgh.harvard.edu>>:
>>> 
>>> mri_info N_Atlas_subcotex.mgz
>> 
>> 
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
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Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz
mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, -1): 
could not open file

> Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. 
> :
> 
> mri_info N_Atlas_subcotex.mgz

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Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Here the results:


pwd:
/Users/boris/Desktop/MirLIND_test/1122/mri

ls -l BN_Atlas_subcotex.mgz:
-rwxrwxrwx  1 boris  staff  37013 13 Aug 23:30 BN_Atlas_subcotex.mgz

Best,
Boris
> Am 13.12.2019 um 23:53 schrieb Greve, Douglas N.,Ph.D. 
> :
> 
> pwd

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Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

yes to both. I always get the error ERROR: cannot find aseg...

On Fri, Dec 13, 2019 at 12:58 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Are you running this from 1122/mri and is BN_Atlas_subcotex.mgz in that
> folder?
>
> On 12/12/19 12:57 PM, Boris Rauchmann wrote:
> >
> > External Email - Use Caution
> >
> > My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg
> > BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
> > SUBJECTS_DIR /Users/boris/Desktop/mydir
> > subject 1122
> > outvol aparc+BN_Atlas_subcotex.mgz
> > useribbon 0
> > baseoffset 0
> > RipUnknown 0
> >
> > Reading lh white surface
> >  /Users/boris/Desktop/mydir/1122/surf/lh.white
> >
> > Reading lh pial surface
> >  /Users/boris/Desktop/mydir/1122/surf/lh.pial
> >
> > Loading lh annotations from
> > /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot
> > 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 rh white surface
> >  /Users/boris/Desktop/mydir/1122/surf/rh.white
> >
> > Reading rh pial surface
> >  /Users/boris/Desktop/mydir/1122/surf/rh.pial
> >
> > Loading rh annotations from
> > /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot
> > reading colortable from annotation file...
> > colortable with 36 entries read (originally
> >
> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
> > Have color table for lh white annotation
> > Have color table for rh white annotation
> > Loading ribbon segmentation from
> > /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
> >
> > Building hash of lh white
> >
> > Building hash of lh pial
> >
> > Building hash of rh white
> >
> > Building hash of rh pial
> > ERROR: cannot find aseg
> >
> >
> > I get the same result using aseg.mgz
> >
> > Thanks,
> > Boris
> >> Am 12.12.2019 um 17:37 schrieb Bruce Fischl
> >> mailto:fis...@nmr.mgh.harvard.edu>>:
> >>
> >> Hi Boris
> >>
> >> can you send us the full command line and screen output of the
> >> commands that are failing?
> >>
> >> cheers
> >> Bruce
> >> On Thu, 12 Dec 2019, Boris Rauchmann wrote:
> >>
> >>> External Email - Use Caution
> >>> Thanks. unfortunately I get an error message when I use the --aseg
> >>> flag for BN_Atlas_subcotex.mgz but
> >>> even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg
> >>> .../fs_all_subjects/xyz/mri/aseg.mgz
> >>> The file BN_Atlas_subcotex.mgz was created using:
> >>> mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
> >>> $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
> >>> $SUBJECTS_DIR/BN_Atlas_subcortex.gca
> >>> $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz
> >>> Best,
> >>> Boris
> >>> On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D.
> >>> mailto:dgr...@mgh.harvard.edu>> wrote:
> >>>  What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with
> >>> your
> >>>  subcortical ROIs added? If so, you can try merging it with the
> >>> aparc, eg,
> >>>
> >>>  mri_aparc2aseg --s subject --volmask --aseg
> >>> BN_Atlas_subcotex.mgz --o
> >>>  aparc+BN_Atlas_subcotex.mgz
> >>>
> >>>  Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg,
> >>> and then
> >>>  run gtmseg as you have done below.
> >>>
> >>>  Let me know if that works
> >>>  doug
> >>>
> >>>  On 12/2/19 1:18 PM, Boris Rauchmann wrote:
> >>>  >
> >>>  > External Email - Use Caution
> >>>  >
> >>>  > In this example tried it with only the subcortical
> >>> segmentations from
> >>>  > my atlas. Please find the logfile attached. It gives me back:
> >>> "tissue
> >>>  > type is not set" but I set it to 2 in the LUT.txt
> >>>  >
> >>>  > In principle look the following commands right to you?
> >>>  >
> >>>  > xcerebralseg --s 0120test --o a

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg 
BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
SUBJECTS_DIR /Users/boris/Desktop/mydir
subject 1122
outvol aparc+BN_Atlas_subcotex.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /Users/boris/Desktop/mydir/1122/surf/lh.white

Reading lh pial surface 
 /Users/boris/Desktop/mydir/1122/surf/lh.pial

Loading lh annotations from /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot
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 rh white surface 
 /Users/boris/Desktop/mydir/1122/surf/rh.white

Reading rh pial surface 
 /Users/boris/Desktop/mydir/1122/surf/rh.pial

Loading rh annotations from /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial
ERROR: cannot find aseg


I get the same result using aseg.mgz 

Thanks,
Boris
> Am 12.12.2019 um 17:37 schrieb Bruce Fischl :
> 
> Hi Boris
> 
> can you send us the full command line and screen output of the commands that 
> are failing?
> 
> cheers
> Bruce
> On Thu, 12 Dec 2019, Boris Rauchmann wrote:
> 
>> External Email - Use Caution
>> Thanks. unfortunately I get an error message when I use the --aseg flag for 
>> BN_Atlas_subcotex.mgz but
>> even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg
>> .../fs_all_subjects/xyz/mri/aseg.mgz
>> The file BN_Atlas_subcotex.mgz was created using: 
>> mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
>> $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
>> $SUBJECTS_DIR/BN_Atlas_subcortex.gca
>> $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz
>> Best,
>> Boris
>> On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. 
>>  wrote:
>>  What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your
>>  subcortical ROIs added? If so, you can try merging it with the aparc, 
>> eg,
>> 
>>  mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o
>>  aparc+BN_Atlas_subcotex.mgz
>> 
>>  Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and then
>>  run gtmseg as you have done below.
>> 
>>  Let me know if that works
>>  doug
>> 
>>  On 12/2/19 1:18 PM, Boris Rauchmann wrote:
>>  >
>>  > External Email - Use Caution
>>  >
>>  > In this example tried it with only the subcortical segmentations from
>>  > my atlas. Please find the logfile attached. It gives me back: "tissue
>>  > type is not set" but I set it to 2 in the LUT.txt
>>  >
>>  > In principle look the following commands right to you?
>>  >
>>  > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m
>>  > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
>>  >
>>  > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab
>>  > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
>>  >
>>  > Ideally I would have a gtmseg with both, the subcortical and the
>>  > cortical structures, but only the subcortical would also be fine as
>>  > long as I can get  mri_gtmpvc running on it.
>>  >
>>  > Thanks,
>>  > Boris
>>  >
>>  > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D.
>>  > mailto:dgr...@mgh.harvard.edu>> wrote:
>>  >
>>  > Can you send the log file for each of the gtmseg runs?
>>  >
>>  > On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
>>  >>
>>  >> External Email - Use Caution
>>  >>
>>  >> Thank you! I have a gca for subcortical  and two gcs (lh/rh) for
>>  >> cortical structures.
>>  >> I created an annot (rh/lh) and a mgz using mris_ca_label
>>  >> and mri_ca_label for parcellation/segmentation stats.
>>  >>
>>  >> For the PET analysis I have the following problem:
>>  >>
>>  

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Thanks. unfortunately I get an error message when I use the --aseg flag for
BN_Atlas_subcotex.mgz but even, if I'm using the original aseg.mgz I get:
ERROR: cannot find aseg .../fs_all_subjects/xyz/mri/aseg.mgz

The file BN_Atlas_subcotex.mgz was created using:
mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
$SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz

Best,
Boris

On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your
> subcortical ROIs added? If so, you can try merging it with the aparc, eg,
>
> mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o
> aparc+BN_Atlas_subcotex.mgz
>
> Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and then
> run gtmseg as you have done below.
>
> Let me know if that works
> doug
>
>
> On 12/2/19 1:18 PM, Boris Rauchmann wrote:
> >
> > External Email - Use Caution
> >
> > In this example tried it with only the subcortical segmentations from
> > my atlas. Please find the logfile attached. It gives me back: "tissue
> > type is not set" but I set it to 2 in the LUT.txt
> >
> > In principle look the following commands right to you?
> >
> > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m
> > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
> >
> > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab
> > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
> >
> > Ideally I would have a gtmseg with both, the subcortical and the
> > cortical structures, but only the subcortical would also be fine as
> > long as I can get  mri_gtmpvc running on it.
> >
> > Thanks,
> > Boris
> >
> > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > Can you send the log file for each of the gtmseg runs?
> >
> > On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
> >>
> >> External Email - Use Caution
> >>
> >> Thank you! I have a gca for subcortical  and two gcs (lh/rh) for
> >> cortical structures.
> >> I created an annot (rh/lh) and a mgz using mris_ca_label
> >> and mri_ca_label for parcellation/segmentation stats.
> >>
> >> For the PET analysis I have the following problem:
> >>
> >> If I use this command: gtmseg --s test --o test.mgz --ctab
> >> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz
> >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
> >>
> >> It gives me the right regions for subcortical structures but it
> >> looks like it uses the standard FS parcellation with my labels
> >> for the cortical parcellations (only 93 cortical regions instead
> >> of 210).
> >>
> >> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz
> >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
> >> --no-xcerseg I get all my 210 cortical parcellations but the
> >> standard FS subcortical segmentations.
> >>
> >> How can I use both in one gtmseg so that I can proceed with it
> >> doing my PET analysis in PETSurfer? It is not totally clear for
> >> me what to merge using xcerebralseg.
> >>
> >> Thanks a lot!
> >>
> >> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D.
> >> mailto:dgr...@mgh.harvard.edu>> wrote:
> >>
> >> It gets the subcortical from apas+head.mgz which gets created
> >> along the
> >> way by xcerebralseg. You can create your own with
> >> xcerebralseg by
> >> specifying your volume as the mergevol. I think this will
> >> work, but I'm
> >> not sure. I'm assuming you've used the GCA to create your own
> >> subcortical seg for the given subject
> >>
> >> On 11/5/19 1:06 PM, Boris Rauchmann wrote:
> >> >
> >> > External Email - Use Caution
> >> >
> >> > I just realized that the above mentioned command (gtmseg
> >> --s XYZ --o
> >> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> >> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
> >> --no-xcerseg)
> >&

Re: [Freesurfer] PETSurfer individual atlas for subcortocal segmentation

[Boris Rauchmann]

External Email - Use Caution

Dear Doug,

thank you for your effort. Let me know if you have any updates on this.

Best,
Boris

On Fri, Dec 6, 2019 at 5:45 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Hi Boris, I'll try to get to it today. Unfortunately, I think this is
> going to require a fair amount of effort on my part. When I wrote this part
> of PETsurfer, I just did not make it super flexible.
> doug
>
>
> On 12/5/2019 10:17 PM, Boris Rauchmann wrote:
>
> External Email - Use Caution
> Did you already have the time to look at the logfile? Do you have any
> suggestions how to proceed?
>
> Thank you!
>
> Am 02.12.2019 um 19:18 schrieb Boris Rauchmann 
> :
>
> 
> In this example tried it with only the subcortical segmentations from my
> atlas. Please find the logfile attached. It gives me back: "tissue type is
> not set" but I set it to 2 in the LUT.txt
>
> In principle look the following commands right to you?
>
> xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m
> BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
>
> gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab
> subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
>
> Ideally I would have a gtmseg with both, the subcortical and the cortical
> structures, but only the subcortical would also be fine as long as I can
> get  mri_gtmpvc running on it.
>
> Thanks,
> Boris
>
> On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> Can you send the log file for each of the gtmseg runs?
>>
>> On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
>>
>> External Email - Use Caution
>> Thank you! I have a gca for subcortical  and two gcs (lh/rh) for cortical
>> structures.
>> I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label
>> for parcellation/segmentation stats.
>>
>> For the PET analysis I have the following problem:
>>
>> If I use this command: gtmseg --s test --o test.mgz --ctab
>> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz --ctx-annot
>> BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
>>
>> It gives me the right regions for subcortical structures but it looks
>> like it uses the standard FS parcellation with my labels for the cortical
>> parcellations (only 93 cortical regions instead of 210).
>>
>> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz --ctx-annot
>> BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' --no-xcerseg I get all my
>> 210 cortical parcellations but the standard FS subcortical segmentations.
>>
>> How can I use both in one gtmseg so that I can proceed with it doing my
>> PET analysis in PETSurfer? It is not totally clear for me what to merge
>> using xcerebralseg.
>>
>> Thanks a lot!
>>
>> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. <
>> dgr...@mgh.harvard.edu> wrote:
>>
>>> It gets the subcortical from apas+head.mgz which gets created along the
>>> way by xcerebralseg. You can create your own with xcerebralseg by
>>> specifying your volume as the mergevol. I think this will work, but I'm
>>> not sure. I'm assuming you've used the GCA to create your own
>>> subcortical seg for the given subject
>>>
>>> On 11/5/19 1:06 PM, Boris Rauchmann wrote:
>>> >
>>> > External Email - Use Caution
>>> >
>>> > I just realized that the above mentioned command (gtmseg --s XYZ --o
>>> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
>>> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg)
>>> > gives me only the cortical segmentation. Is there any way to also
>>> > include the subcortical segmentation based on my individual atlas? I
>>> > also have an Atlas_subcortex.gca file available.
>>> >
>>> > Best,
>>> > Boris
>>> >
>>> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D.
>>> > mailto:dgr...@mgh.harvard.edu>> wrote:
>>> >
>>> > There is no cut off for the minimum size. As it gets smaller, the
>>> PVC
>>> > noise amplification will become bigger (it also depends on the
>>> > shape as
>>> > well).
>>> >
>>> > I think the --no-xcerseg is the right way to go now
>>> >
>>> > On 8/13/19 11:00 AM, Boris Rauchmann wrote:
>>> > >
>>> > > External Email - Use Caution
>>> > >
>

Re: [Freesurfer] PETSurfer individual atlas for subcortocal segmentation

[Boris Rauchmann]

External Email - Use Caution

Did you already have the time to look at the logfile? Do you have any 
suggestions how to proceed?

Thank you!

> Am 02.12.2019 um 19:18 schrieb Boris Rauchmann :
> 
> 
> In this example tried it with only the subcortical segmentations from my 
> atlas. Please find the logfile attached. It gives me back: "tissue type is 
> not set" but I set it to 2 in the LUT.txt
> 
> In principle look the following commands right to you?
> 
> xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m 
> BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
> 
> gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab subcort_BN_LUT.txt 
> --o gtmseg+subcort_BN.mgz
> 
> Ideally I would have a gtmseg with both, the subcortical and the cortical 
> structures, but only the subcortical would also be fine as long as I can get  
> mri_gtmpvc running on it. 
> 
> Thanks,
> Boris
> 
>> On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. 
>>  wrote:
>> Can you send the log file for each of the gtmseg runs?
>> 
>>> On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
>>> External Email - Use Caution
>>> 
>>> Thank you! I have a gca for subcortical  and two gcs (lh/rh) for cortical 
>>> structures. 
>>> I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label 
>>> for parcellation/segmentation stats. 
>>> 
>>> For the PET analysis I have the following problem:
>>> 
>>> If I use this command: gtmseg --s test --o test.mgz --ctab 
>>> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz --ctx-annot 
>>> BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' 
>>> 
>>> It gives me the right regions for subcortical structures but it looks like 
>>> it uses the standard FS parcellation with my labels for the cortical 
>>> parcellations (only 93 cortical regions instead of 210). 
>>> 
>>> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz --ctx-annot 
>>> BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' --no-xcerseg I get all my 
>>> 210 cortical parcellations but the standard FS subcortical segmentations. 
>>> 
>>> How can I use both in one gtmseg so that I can proceed with it doing my PET 
>>> analysis in PETSurfer? It is not totally clear for me what to merge using 
>>> xcerebralseg.
>>> 
>>> Thanks a lot!
>>> 
>>>> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. 
>>>>  wrote:
>>>> It gets the subcortical from apas+head.mgz which gets created along the 
>>>> way by xcerebralseg. You can create your own with xcerebralseg by 
>>>> specifying your volume as the mergevol. I think this will work, but I'm 
>>>> not sure. I'm assuming you've used the GCA to create your own 
>>>> subcortical seg for the given subject
>>>> 
>>>> On 11/5/19 1:06 PM, Boris Rauchmann wrote:
>>>> >
>>>> > External Email - Use Caution
>>>> >
>>>> > I just realized that the above mentioned command (gtmseg --s XYZ --o 
>>>> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab 
>>>> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg) 
>>>> > gives me only the cortical segmentation. Is there any way to also 
>>>> > include the subcortical segmentation based on my individual atlas? I 
>>>> > also have an Atlas_subcortex.gca file available.
>>>> >
>>>> > Best,
>>>> > Boris
>>>> >
>>>> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. 
>>>> > mailto:dgr...@mgh.harvard.edu>> wrote:
>>>> >
>>>> > There is no cut off for the minimum size. As it gets smaller, the PVC
>>>> > noise amplification will become bigger (it also depends on the
>>>> > shape as
>>>> > well).
>>>> >
>>>> > I think the --no-xcerseg is the right way to go now
>>>> >
>>>> > On 8/13/19 11:00 AM, Boris Rauchmann wrote:
>>>> > >
>>>> > > External Email - Use Caution
>>>> > >
>>>> > > Thank you for your prompt answer - the command worked. This is the
>>>> > > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html
>>>> > > What is approximately the smallest possible segment when using PVC?
>>>> >  

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

In this example tried it with only the subcortical segmentations from my
atlas. Please find the logfile attached. It gives me back: "tissue type is
not set" but I set it to 2 in the LUT.txt

In principle look the following commands right to you?

xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m
BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca

gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab
subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz

Ideally I would have a gtmseg with both, the subcortical and the cortical
structures, but only the subcortical would also be fine as long as I can
get  mri_gtmpvc running on it.

Thanks,
Boris

On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Can you send the log file for each of the gtmseg runs?
>
> On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
>
> External Email - Use Caution
> Thank you! I have a gca for subcortical  and two gcs (lh/rh) for cortical
> structures.
> I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label
> for parcellation/segmentation stats.
>
> For the PET analysis I have the following problem:
>
> If I use this command: gtmseg --s test --o test.mgz --ctab
> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz --ctx-annot
> BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
>
> It gives me the right regions for subcortical structures but it looks like
> it uses the standard FS parcellation with my labels for the cortical
> parcellations (only 93 cortical regions instead of 210).
>
> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz --ctx-annot
> BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' --no-xcerseg I get all my
> 210 cortical parcellations but the standard FS subcortical segmentations.
>
> How can I use both in one gtmseg so that I can proceed with it doing my
> PET analysis in PETSurfer? It is not totally clear for me what to merge
> using xcerebralseg.
>
> Thanks a lot!
>
> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> It gets the subcortical from apas+head.mgz which gets created along the
>> way by xcerebralseg. You can create your own with xcerebralseg by
>> specifying your volume as the mergevol. I think this will work, but I'm
>> not sure. I'm assuming you've used the GCA to create your own
>> subcortical seg for the given subject
>>
>> On 11/5/19 1:06 PM, Boris Rauchmann wrote:
>> >
>> > External Email - Use Caution
>> >
>> > I just realized that the above mentioned command (gtmseg --s XYZ --o
>> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
>> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg)
>> > gives me only the cortical segmentation. Is there any way to also
>> > include the subcortical segmentation based on my individual atlas? I
>> > also have an Atlas_subcortex.gca file available.
>> >
>> > Best,
>> > Boris
>> >
>> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D.
>> > mailto:dgr...@mgh.harvard.edu>> wrote:
>> >
>> > There is no cut off for the minimum size. As it gets smaller, the
>> PVC
>> > noise amplification will become bigger (it also depends on the
>> > shape as
>> > well).
>> >
>> > I think the --no-xcerseg is the right way to go now
>> >
>> > On 8/13/19 11:00 AM, Boris Rauchmann wrote:
>> > >
>> > > External Email - Use Caution
>> > >
>> > > Thank you for your prompt answer - the command worked. This is the
>> > > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html
>> > > What is approximately the smallest possible segment when using
>> PVC?
>> > > Also, does the exclusion of extracerebral structures harm? I
>> > used that
>> > > flag because it complained:
>> > >
>> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
>> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
>> > > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok
>> > > but you must indicate whether to use what is there (--no-xcerseg)
>> > > or create a new one and overwrite what is there (--xcerseg)
>> > > or specify your own headseg (--head)
>> > >
>> > > and did not want to override my apas+head.mgz
>> > >
>> > > Thanks,

[Freesurfer] Using individual atlas in PETSurfer

[Boris Rauchmann]

External Email - Use Caution

Dear all,

I have a LUT, a gca file for subcortical segmentation and two gcs files for
parcellation available. How can I get SUVRs for both the cortical and
subcortical structures?

I  tried using xcerebralseg to create a individual segmentation to replace
the apas+head.mgz but when I'm using gtmseg I only managed it to get
results for the cortical parcellation using a annot created from the two
gcs files (--ctx-annot atlas --ctab LUT). Can someone help me with this?

Best,
Boris
___
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Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Thank you! I have a gca for subcortical  and two gcs (lh/rh) for cortical
structures.
I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label
for parcellation/segmentation stats.

For the PET analysis I have the following problem:

If I use this command: gtmseg --s test --o test.mgz --ctab
/xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz --ctx-annot
BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'

It gives me the right regions for subcortical structures but it looks like
it uses the standard FS parcellation with my labels for the cortical
parcellations (only 93 cortical regions instead of 210).

If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz --ctx-annot
BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt' --no-xcerseg I get all my
210 cortical parcellations but the standard FS subcortical segmentations.

How can I use both in one gtmseg so that I can proceed with it doing my PET
analysis in PETSurfer? It is not totally clear for me what to merge using
xcerebralseg.

Thanks a lot!

On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> It gets the subcortical from apas+head.mgz which gets created along the
> way by xcerebralseg. You can create your own with xcerebralseg by
> specifying your volume as the mergevol. I think this will work, but I'm
> not sure. I'm assuming you've used the GCA to create your own
> subcortical seg for the given subject
>
> On 11/5/19 1:06 PM, Boris Rauchmann wrote:
> >
> > External Email - Use Caution
> >
> > I just realized that the above mentioned command (gtmseg --s XYZ --o
> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg)
> > gives me only the cortical segmentation. Is there any way to also
> > include the subcortical segmentation based on my individual atlas? I
> > also have an Atlas_subcortex.gca file available.
> >
> > Best,
> > Boris
> >
> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > There is no cut off for the minimum size. As it gets smaller, the PVC
> > noise amplification will become bigger (it also depends on the
> > shape as
> > well).
> >
> > I think the --no-xcerseg is the right way to go now
> >
> > On 8/13/19 11:00 AM, Boris Rauchmann wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Thank you for your prompt answer - the command worked. This is the
> > > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html
> > > What is approximately the smallest possible segment when using PVC?
> > > Also, does the exclusion of extracerebral structures harm? I
> > used that
> > > flag because it complained:
> > >
> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
> > > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok
> > > but you must indicate whether to use what is there (--no-xcerseg)
> > > or create a new one and overwrite what is there (--xcerseg)
> > > or specify your own headseg (--head)
> > >
> > > and did not want to override my apas+head.mgz
> > >
> > > Thanks,
> > > Boris
> > >
> > > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D.
> > > mailto:dgr...@mgh.harvard.edu>
> > <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>>
> > wrote:
> > >
> >     >     I don't know what the Brainnetome is, but it looks like you
> have
> > > it in
> > > annotation form. I think that command should work. Why are
> > you using
> > > --no-xcerseg? This will cause it to not include extracerebral
> > > structures. Also note that you cannot use arbitrarily small
> > segments
> > > when doing PVC.
> > >
> > > On 8/13/19 10:26 AM, Boris Rauchmann wrote:
> > > >
> > > > External Email - Use Caution
> > > >
> > > > Dear all,
> > > >
> > > > my intention is to use the Brainnetome Atlas
> > > parcellation/segmentation
> > > > in PETSurfer to obtain PVC corrected SUVRs for the atlas
> > ROIs. I
> > > used:

Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

I just realized that the above mentioned command (gtmseg --s XYZ --o
BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
'/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg) gives
me only the cortical segmentation. Is there any way to also include the
subcortical segmentation based on my individual atlas? I also have an
Atlas_subcortex.gca file available.

Best,
Boris

On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> There is no cut off for the minimum size. As it gets smaller, the PVC
> noise amplification will become bigger (it also depends on the shape as
> well).
>
> I think the --no-xcerseg is the right way to go now
>
> On 8/13/19 11:00 AM, Boris Rauchmann wrote:
> >
> > External Email - Use Caution
> >
> > Thank you for your prompt answer - the command worked. This is the
> > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html
> > What is approximately the smallest possible segment when using PVC?
> > Also, does the exclusion of extracerebral structures harm? I used that
> > flag because it complained:
> >
> > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
> > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok
> > but you must indicate whether to use what is there (--no-xcerseg)
> > or create a new one and overwrite what is there (--xcerseg)
> > or specify your own headseg (--head)
> >
> > and did not want to override my apas+head.mgz
> >
> > Thanks,
> > Boris
> >
> > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > I don't know what the Brainnetome is, but it looks like you have
> > it in
> > annotation form. I think that command should work. Why are you using
> > --no-xcerseg? This will cause it to not include extracerebral
> > structures. Also note that you cannot use arbitrarily small segments
> > when doing PVC.
> >
> > On 8/13/19 10:26 AM, Boris Rauchmann wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Dear all,
> > >
> > > my intention is to use the Brainnetome Atlas
> > parcellation/segmentation
> > > in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I
> > used:
> > >
> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg
> > >
> > > Is this the right approach to obtain a high resolution
> > segmentation to
> > > run PVC methods?
> > >
> > > Thanks,
> > > Boris
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  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
>
>
> ___
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Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Alright, thanks!

On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> There is no cut off for the minimum size. As it gets smaller, the PVC
> noise amplification will become bigger (it also depends on the shape as
> well).
>
> I think the --no-xcerseg is the right way to go now
>
> On 8/13/19 11:00 AM, Boris Rauchmann wrote:
> >
> > External Email - Use Caution
> >
> > Thank you for your prompt answer - the command worked. This is the
> > atlas mentioned: http://atlas.brainnetome.org/brainnetome.html
> > What is approximately the smallest possible segment when using PVC?
> > Also, does the exclusion of extracerebral structures harm? I used that
> > flag because it complained:
> >
> > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
> > ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok
> > but you must indicate whether to use what is there (--no-xcerseg)
> > or create a new one and overwrite what is there (--xcerseg)
> > or specify your own headseg (--head)
> >
> > and did not want to override my apas+head.mgz
> >
> > Thanks,
> > Boris
> >
> > On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > I don't know what the Brainnetome is, but it looks like you have
> > it in
> > annotation form. I think that command should work. Why are you using
> > --no-xcerseg? This will cause it to not include extracerebral
> > structures. Also note that you cannot use arbitrarily small segments
> > when doing PVC.
> >
> > On 8/13/19 10:26 AM, Boris Rauchmann wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Dear all,
> > >
> > > my intention is to use the Brainnetome Atlas
> > parcellation/segmentation
> > > in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I
> > used:
> > >
> > > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> > > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg
> > >
> > > Is this the right approach to obtain a high resolution
> > segmentation to
> > > run PVC methods?
> > >
> > > Thanks,
> > > Boris
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  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
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Thank you for your prompt answer - the command worked. This is the atlas
mentioned: http://atlas.brainnetome.org/brainnetome.html
What is approximately the smallest possible segment when using PVC?
Also, does the exclusion of extracerebral structures harm? I used that flag
because it complained:

gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
'/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
ERROR: /media/subjects/XYZ/mri/apas+head.mgz exists. This is ok
but you must indicate whether to use what is there (--no-xcerseg)
or create a new one and overwrite what is there (--xcerseg)
or specify your own headseg (--head)

and did not want to override my apas+head.mgz

Thanks,
Boris

On Tue, Aug 13, 2019 at 4:44 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> I don't know what the Brainnetome is, but it looks like you have it in
> annotation form. I think that command should work. Why are you using
> --no-xcerseg? This will cause it to not include extracerebral
> structures. Also note that you cannot use arbitrarily small segments
> when doing PVC.
>
> On 8/13/19 10:26 AM, Boris Rauchmann wrote:
> >
> > External Email - Use Caution
> >
> > Dear all,
> >
> > my intention is to use the Brainnetome Atlas parcellation/segmentation
> > in PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I used:
> >
> > gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg
> >
> > Is this the right approach to obtain a high resolution segmentation to
> > run PVC methods?
> >
> > Thanks,
> > Boris
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
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[Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Dear all,

my intention is to use the Brainnetome Atlas parcellation/segmentation in
PETSurfer to obtain PVC corrected SUVRs for the atlas ROIs. I used:

gtmseg --s XYZ --o BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
'/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt' --no-xcerseg

Is this the right approach to obtain a high resolution segmentation to run
PVC methods?

Thanks,
Boris
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[Freesurfer] Group mean tracer uptake images

[Boris Rauchmann]

External Email - Use Caution

Dear FS community,

how can I create group mean tracer uptake images in surface space with FS from 
several overlays?

Thanks,
Boris

Von meinem iPhone gesendet

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[Freesurfer] scan acquisition date from recon all

[Boris Rauchmann]

External Email - Use Caution

Dear all,

is there any way to find the scan acquisition date in the recon-all log?

Thanks,
Boris
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[Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

[Boris Rauchmann]

External Email - Use Caution

Dear all,

depends the Segmentation of hippocampal subfields and nuclei of the amygdala 
pipeline on the fs-recon all pipeline? I made some changes mainly by defining 
control points to fix intensity normalization in my dataset and rerun recon 
all. I´m not sure if I also have to rerun the subfields pipeline now?

Thanks, 
Boris

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[Freesurfer] PetSurfer gtmpvc

[Boris Rauchmann]

External Email - Use Caution

Hi all,

is there a way to easily get the volume stats for all regions after pvc
correction using mri_gtmpvc ? I think its not included in gtm.stats.dat.

Thanks,
Boris
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Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Alright, thanks I confused that. I already found a better way for my purposes. 
Im just running mri_gtmpvc using the flags —psf=0 and —no-tfe to get the non 
PVC subcortical SUVs.

> Am 17.05.2019 um 17:28 schrieb Greve, Douglas N.,Ph.D. 
> :
> 
> In mri_segstats, use --seg $SUBJECTS_DIR/xyz/mri/aparc+aseg.mgz 
> --ctab-default ...
> when you use --annot, you are saying that the input is on the surface.
> 
> On 5/17/2019 9:07 AM, Boris Rauchmann wrote:
>> External Email - Use Caution
>> 
>> Dear Freesurfer community,
>> 
>> I am trying to extract SUV values from sub-cortical segmentation or gtmseg I 
>> don t want to use any PVC. 
>> 
>> I used the following commands:
>> 
>> gtmseg --s xyz
>> 
>> then 
>> mri_coreg --s xyz --mov abetapet.nii.gz --reg abetapet.reg.lta
>> 
>> following
>> mri_vol2vol --mov abetapet.nii
>>  --reg abetapet.reg.lta --targ orig.mgz --o abetapet.sm00.nii.gz
>> and
>> 
>> mri_segstats  --annot
>>  xyz lh gtmseg --i abetapet.sm00.nii.gz --sum xyz_abeta.stats
>> 
>> resulting in this dimension mismatch error:
>> input 256 256 256
>>   seg   416 450 476
>> 
>> Is that the correct way for doing this analysis? any suggestions how to 
>> solve the mismatch error?
>> 
>> Thanks,
>> Boris
>> 
>> 
>> ___
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>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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[Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Dear Freesurfer community,

I am trying to extract SUV values from sub-cortical segmentation or gtmseg
I don t want to use any PVC.

I used the following commands:

gtmseg --s xyz

then
mri_coreg --s xyz --mov abetapet.nii.gz --reg abetapet.reg.lta

following


mri_vol2vol --mov abetapet.nii --reg abetapet.reg.lta --targ orig.mgz --o
abetapet.sm00.nii.gz


and

mri_segstats  --annot xyz lh gtmseg --i abetapet.sm00.nii.gz --sum
xyz_abeta.stats

resulting in this dimension mismatch error:
input 256 256 256
  seg   416 450 476

Is that the correct way for doing this analysis? any suggestions how to
solve the mismatch error?

Thanks,
Boris
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[Freesurfer] recon-all error after maual control points definition

[Boris Rauchmann]

External Email - Use Caution

reading input surface xyz/fs_all_subjects/0031/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Reading original properties of orig.nofix
Reading vertex positions of inflated.nofix
Computing Initial Surface Statistics
  -face   loglikelihood: -9.3220  (-4.6610)
  -vertex loglikelihood: -6.6151  (-3.3076)
  -normal dot loglikelihood: -3.5637  (-3.5637)
  -quad curv  loglikelihood: -6.1122  (-3.0561)
  Total Loglikelihood : -25.6131

CORRECTING DEFECT 0 (vertices=16503, convex hull=4824, v0=77)
mrisAddEdge: too many edges (255)
XL defect detected...
Large defect found - not a problem, but a curiousity
No such file or directory
Linux linuxrechner 4.15.0-47-generic #50~16.04.1-Ubuntu SMP Fri Mar 15
16:06:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 0031 exited with ERRORS at Sun Apr 14 16:45:47 CEST 2019

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Any idea what causes this problem?

Thank you,

Boris
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[Freesurfer] PETSurfer and thickness data

[Boris Rauchmann]

External Email - Use Caution

Dear FS community,

I would like to assess how PET tracer uptake is related to thickness changes in 
AD patients. Is it possible to generate difference maps for both methods and 
run a GLM? Or would you suggest another approach?

Thanks,
Boris

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[Freesurfer] mri_coreg error

[Boris Rauchmann]

External Email - Use Caution

Hi FreeSurfer community,

when I run mri_coreg I get the following error.
 /XYZ/2123/mri/brainmask.mgz is in the specified location.

Can you help me with this?

Thanks!
Boris

mri_coreg --s 2123 --mov /XYZ/2123.nii --reg 2123.reg.lta
Could not set locale
No such file or directory
Could not set locale

$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $
cwd /home/demenzbild
cmdline mri_coreg --s 2123 --mov /XYZ/2123.nii --reg 2123.reg.lta
sysname  Linux
hostname XXX
machine  x86_64
user d
dof6
nsep2
cras01
ftol0.00
linmintol0.001000
bf   1
bflim30.00
bfnsamp30
SmoothRef 0
SatPct99.99
MovOOB 0
optschema 1
Reading in mov /XYZ/2123.nii
WARNING: 78694 NaNs found in volume /XYZ/2123.nii...

No such file or directory
Reading in ref /XYZ/2123/mri/brainmask.mgz
mghRead(/XYZ/2123/mri/brainmask.mgz, -1): could not open file
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[Freesurfer] -so unknown in mri_surf2vol?

[Boris Rauchmann]

External Email - Use Caution

My_pc$ mri_surf2vol --o 0021_thickness-in-volume.nii.gz --subject 0021 \ --so 
$SUBJECTS_DIR/0021/surf/lh.white $SUBJECTS_DIR/0021/surf/lh.thickness \ --so 
$SUBJECTS_DIR/0021/surf/rh.white $SUBJECTS_DIR/0021/surf/rh.thickness

ERROR: Option  --so unknown

Why it returns that —so is unknown? Exactly this line is given as an example 
on: 
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol#ArgumentsforBothMethods 


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Re: [Freesurfer] cortical thickness calculation based on hammersmith segmentation

[Boris Rauchmann]

External Email - Use Caution

Hi Bruce,

thank you for your quick answer. I managed it now to create cannot files based 
on the atlas volumetric segmentations.

I first created:

mri_vol2surf —src  .../Hammers_mith_atlas_n30r83_SPM5.nii --out 
.../Hammers_AVG.nii --out_type mgh --hemi lh --mni152reg

then applied:

mris_apply_reg --src .../hammers_lh_avg_surf.mgh --trg 
.../hammers_lh_INDI_0021.mgh --streg $SUBJECTS_DIR/fsaverage/surf/lh.sphere.reg 
 .../0021/surf/lh.sphere 

and:

mris_seg2annot --seg /.../hammers_lh_INDI_0021.mgh   --s 0021 --h lh --ctab 
/.../ExploreDTI_Pcode/Source/Misc/My_FS_LUT.txt  --o 
.../lh.hammersmithINDI.annot

My question now is how can I create a suitable LUT with the correct labels for 
the cortical parcellations? I have only a .csv file with the labels for the 
volumetric atlas? 

My goal is to use 

mris_anatomical_stats -a .../0021/label/lh.hammersmithINDI.annot -b 0021 lh

to get the cortical thickness values of each segment in the annot for every 
participant file.

Thanks again, 
Boris




> Am 27.01.2019 um 23:58 schrieb Bruce Fischl :
> 
> Hi Boris
> 
> vol2surf samples a scalar overlay in the volume to be a scalar overlay on the 
> surface. This is NOT the same as a surface itself - it contains no geometry 
> or topology information. Try giving freeview a surface (which I guess you 
> have for subject 0021). Something like
> 
> freeview -f \
> 0021/surf/lh.inflated:overlay=lhHammers_mith_atlas_n30r83_SPM5surf.mgh
> 
> cheers
> Bruce
> 
> 
> On Sun, 27 Jan 2019, Boris Rauchmann wrote:
> 
>> External Email - Use Caution
>> Hi,
>> I used the following commands:
>>  mri_vol2surf —src  .../Hammers_mith_atlas_n30r83_SPM5.nii  --out 
>> lhHammers_mith_atlas_n30r83_SPM5surf.mgh
>> --out_type mgh --hemi lh --regheader 0021
>> srcvol = .../Hammers_mith_atlas_n30r83_SPM5.nii
>> srcreg unspecified
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = lh
>> reshape = 0
>> interp = nearest
>> float2int = round
>> GetProjMax = 0
>> INFO: float2int code = 0
>> Done loading volume
>> Computing registration from header.
>>   Using .../0021/mri/orig.mgz as target reference.
>> Reading surface .../0021/surf/lh.white
>> Done reading source surface
>> Mapping Source Volume onto Source Subject Surface
>>  1 0 0 0
>> using old
>> Done mapping volume to surface
>> Number of source voxels hit = 76207
>> Writing to lhHammers_mith_atlas_n30r83_SPM5surf.mgh
>> Dim: 125545 1 1
>> it creates the .mgh file but when I try to open in in Freeview or tksurfer 
>> to check the surface file I get the
>> following error message:
>> my_computer$ freeview
>> ERROR: MRISread: file ‚/.../lhHammers_mith_atlas_n30r83_SPM5surf.mgh' has 0 
>> vertices!
>> Probably trying to use a scalar data file as a surface!
>> nquads=65537,  nvertices=0
>> ERROR: MRISread: file , /…/lhHammers_mith_atlas_n30r83_SPM5surf.mgh' has 
>> many more faces than vertices!
>> Probably trying to use a scalar data file as a surface!
>> [0]PETSC ERROR: 
>> 
>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
>> probably memory access out of range
>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [0]PETSC ERROR: or see 
>> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
>> ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to 
>> find memory corruption errors
>> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and 
>> run 
>> [0]PETSC ERROR: to get more information on the crash.
>> [0]PETSC ERROR: - Error Message 
>> 
>> [0]PETSC ERROR: Signal received!
>> [0]PETSC ERROR: 
>> 
>> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 
>> CDT 2008 HG revision:
>> 4466c6289a0922df26e20626fd4a0b4dd03c8124
>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>> [0]PETSC ERROR: See docs/index.html for manual pages.
>> [0]PETSC ERROR: 
>> 
>> [0]PETSC ERROR: Unknown Name on a darwin12. named my_computer.local by boris 
>> Sun Jan 27 23:12:45 2019
>> [0]PETSC ERROR: Libraries linked from
>> /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-

Re: [Freesurfer] cortical thickness calculation based on hammersmith segmentation

[Boris Rauchmann]

External Email - Use Caution

Hi,

I used the following commands:

 mri_vol2surf —src  .../Hammers_mith_atlas_n30r83_SPM5.nii  --out 
lhHammers_mith_atlas_n30r83_SPM5surf.mgh --out_type mgh --hemi lh --regheader 
0021
srcvol = .../Hammers_mith_atlas_n30r83_SPM5.nii
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using .../0021/mri/orig.mgz as target reference.
Reading surface .../0021/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 0 0 0
using old
Done mapping volume to surface
Number of source voxels hit = 76207
Writing to lhHammers_mith_atlas_n30r83_SPM5surf.mgh
Dim: 125545 1 1


it creates the .mgh file but when I try to open in in Freeview or tksurfer to 
check the surface file I get the following error message:


my_computer$ freeview
ERROR: MRISread: file ‚/.../lhHammers_mith_atlas_n30r83_SPM5surf.mgh' has 0 
vertices!
Probably trying to use a scalar data file as a surface!


nquads=65537,  nvertices=0
ERROR: MRISread: file , /…/lhHammers_mith_atlas_n30r83_SPM5surf.mgh' has many 
more faces than vertices!
Probably trying to use a scalar data file as a surface!

[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find 
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a darwin12. named my_computer.local by boris 
Sun Jan 27 23:12:45 2019
[0]PETSC ERROR: Libraries linked from 
/usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt
[0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 
--download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 
--with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 
FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault


Hoe can I actually check the surface file?

Thanks,
Boris 

> Am 25.01.2019 um 17:45 schrieb Greve, Douglas N.,Ph.D. 
> :
> 
> Those are the commands. Can you send the command lines you used and a fuller 
> description of exactly how it is not working?
> 
> On 1/25/19 10:56 AM, Boris Rauchmann wrote:
>> External Email - Use Caution
>> 
>>  <>Dear FreeSurfer Developers,
>> 
>>  
>> I´m trying to extract the cortical thickness of individuals from a study 
>> cohort based on an hammersmith n30r83 atlas segmentation. I have this atlas 
>> only in as a volumetric file. I already run recon-all on all subjects. I 
>> tried mri_vol2surf and then mris_seg2annot but without success so far. What 
>> commands would you recommend me to run?
>> 
>>  
>> Thanks,
>> 
>> Boris
>> 
>> 
>> 
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[Freesurfer] cortical thickness calculation based on hammersmith segmentation

[Boris Rauchmann]

External Email - Use Caution

 <>Dear FreeSurfer Developers,

 

I´m trying to extract the cortical thickness of individuals from a study cohort 
based on an hammersmith n30r83 atlas segmentation. I have this atlas only in as 
a volumetric file. I already run recon-all on all subjects. I tried 
mri_vol2surf and then mris_seg2annot but without success so far. What commands 
would you recommend me to run?

 

Thanks,

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Re: [Freesurfer] mri_watershed Error

[Boris Rauchmann]

External Email - Use Caution

It would be great if you can have a look at the nu.mgz and talairach.xmf but 
unfortunately I´m not able to provide it in the mailing list.
Is there another way to send you the files?

Thanks, 
Boris

> Am 11.10.2018 um 22:04 schrieb Bruce Fischl :
> 
> Hi Boris
> 
> the input to that watershed call is the T1.mgz, but it is already problematic 
> as you can see from the log. You should take a look at the nu.mgz and make 
> sure it is correct. You can also email me the nu.mgz and the talairach.xfm 
> (in the mri/transforms dir) if you want and I'll take a look
> cheers
> Bruce
> 
> 
> On Thu, 11 Oct 2018, Boris Rauchmann wrote:
> 
>>   External Email - Use Caution 
>> Hi again,
>> 
>> sorry. Please find attached the recon-all.log. I´m not sure how to check the 
>> input to watershed.
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Re: [Freesurfer] mri_watershed Error

[Boris Rauchmann]

External Email - Use Caution

Hi again,

sorry. Please find attached the recon-all.log. I´m not sure how to check the 
input to watershed.  

recon-all.log
Description: Binary data


Thanks,
Boris

> Am 11.10.2018 um 18:55 schrieb Bruce Fischl :
> 
> Hi Boris
> 
> can you check to make sure that the input to the watershed looks ok? Also, in 
> general it is a lot easier for us to help if you send us the full command 
> line and screeen output and attach the recon-all.log
> 
> cheers
> Bruce
> 
> 
> On Thu, 11 Oct 2018, Boris Rauchmann wrote:
> 
>> External Email - Use Caution
>> When I run recon-all i get the follwing error message:
>>  mri_watershed Error: 
>>  GLOBAL region of the brain empty !
>> Linux 02f92500bcfb 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25
>> 08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
>> recon-all -s sub-XYZ exited with ERRORS at Thu Oct 11 15:10:22 UTC 2018
>> The .nii file looks fine. Can someone help me with this? 
>> Best,
>> Boris
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[Freesurfer] mri_watershed Error

[Boris Rauchmann]

External Email - Use Caution

When I run recon-all i get the follwing error message:

 mri_watershed Error:
 GLOBAL region of the brain empty !
Linux 02f92500bcfb 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25
08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-XYZ exited with ERRORS at Thu Oct 11 15:10:22 UTC 2018

The .nii file looks fine. Can someone help me with this?

Best,
Boris
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[Freesurfer] How to deal with different resolutions in recon all and hippocampal subfield segmentation

[Boris Rauchmann]

External Email - Use Caution

Hi,

I'm working on data from different sites, scanned with different
MRI-Scanners ans slightly different parameters (all in the range of 1x1x1
to 1.2x1.2x1). I wonder if you would recommend to run recon all and
segmentation of HC sub-fields in different analysis and how comparable the
results will be.

Thanks,
Tragus
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[Freesurfer] Split a lablemap in the .annot format into parts

[Boris Rauchmann]

Dear FS Community,

is there an easy way to split a lablemap in the .annot format into parts?
In detail I would like to split network 6 (frontoparietal) of the yeo atlas 
(fsaverage/label/rh.Yeo2011_7Networks_N1000.annot) into the frontal, parietal 
and temporal part on each side. 
Is there an easy way to do this in FS? 

Thank you,

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