Re: [Freesurfer] mri_aparc2aseg bad incorrect ROIs

2022-06-21 Thread Benjamin Deck 
External Email - Use Caution

Hi Doug,

I think I may have found a similar issue via the mailing list which I
hadn't noticed before. However, it's not clear to me how to implement this
solution.

https://secure-web.cisco.com/1uK1SqmLnsjHZpvlRJyITHKYUhsrOBcU7gkc7GagN0OUsbxgbuaXR7mJEmN0D9LHVvpNjZScCPthfFK0-9DMt-JMGIobJ0Nwvjv6_dhtQwajnyRV-kWYGhspgxGFAHobEFgm1BMAz6KLv1bPDs0bfsrNkxyEXnOh89JZKO57Zx_8Y28sU2xHewG4MD2qUokz-rsz_Q-LS4Sm1TweiFTdAd5rdvZ1_CIQ58pI-qz5T-dSCp-XWl7LVsG22IpD_nFN8juENy27iFWfgh-2IhA3NYK7kXMdWYfu_s5zrX-0_JlLlPfDnE6F53WSFLralPOyd/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg56796.html




Any ideas?



On Tue, Jun 21, 2022 at 1:48 PM Benjamin Deck  wrote:

> Hi Doug,
>
> Thanks for getting back to me.
>
> Yes, it's very weird. My LUT doesn't contain any subcortical structures
> but when I load my custom LUT into Freeview, it shows my surface-based
> parcellation in the subcortical regions. Furthermore, my annotation files
> look completely fine!
>
> I noticed that the indices of my LUT are the same as the default LUT,
> could this be a problem; should my custom LUT have unique index IDs?
>
> For example see the two LUTs:
>
>
> *FS default LUT:*
> #No. Label Name:R   G   B   A
>
> 0   Unknown 0   0   0   0
> 1   Left-Cerebral-Exterior  70  130 180 0
> 2   Left-Cerebral-White-Matter  245 245 245 0
> 3   Left-Cerebral-Cortex205 62  78  0
> 4   Left-Lateral-Ventricle  120 18  134 0
> 5   Left-Inf-Lat-Vent   196 58  250 0
> 6   Left-Cerebellum-Exterior0   148 0   0
> 7   Left-Cerebellum-White-Matter220 248 164 0
> .
>
> *My Custom LUT*
> 0 Unknown 0 0 0 0
> 1 Net_10_ROIs_1_lh_native 255 255 255 0
> 2 Net_11_ROIs_1_lh_native 25  5   25  0
> 3 Net_12_ROIs_1_lh_native 25  100 40  0
> 4 Net_12_ROIs_2_lh_native 70  130 180 0
> 5 Net_13_ROIs_1_lh_native 100 100 0   0
> 6 Net_13_ROIs_2_lh_native 196 58  250 0
> 7 Net_13_ROIs_3_lh_native 100 25  0   0
> .
>
> *Output from the call with your suggestion of --aseg flag:*
>
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> *mri_aparc2aseg --s sub-DAEK --annot yeo2011 --annot-table
> sub-DAEK_yeoLUT.txt --threads 6 --rip-unknown --volmask --aseg
> aseg.presurf.hyposSUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjectssubject
> sub-DAEKoutvol
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/yeo2011+aseg.mgzuseribbon
> 0baseoffset 0RipUnknown 18 avail.processors, using 6Reading lh white
> surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.whiteReading
> lh pial
> surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.pialLoading
> lh annotations from
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annotHave
> color table for lh white annotationRipping vertices labeled as unkownRipped
> 27062 vertices from left hemiBuilding hash of lh whiteBuilding hash of lh
> pialReading rh white
> surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.whiteReading
> rh pial
> surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.pialLoading
> rh annotations from
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/rh.yeo2011.annotHave
> color table for rh white annotationRipping vertices labeled as unkownRipped
> 27560 vertices from right hemiBuilding hash of rh whiteBuilding hash of rh
> pialLoading ribbon segmentation from
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgzLoading aseg
> from
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/aseg.presurf.hypos.mgzASeg
> Vox2RAS: 0.8   0.0   0.0   127.9; 0.0
> 0.0   0.8  -127.9; 0.0  -0.8   0.0
> 127.9; 0.0   0.0   0.0
> 1.0;-Labeling Slice (320)161 108 214  54   0
> 267   1  55 268   2 269  56   3 270  57   4 271  58 272   5  59  6 273  60
>   7 274  61 275   8  62 276   9  63 277  10  64 278  11  65 279 12  66 280
>  67  13 281  68  14 282  15  69 283  16 284  70  17 285  18 286  19287  20
>  71 288  21 289  22 290  23 291  24 292  25 293  26 294  27 295  28  72 296
>  29 297  30 298  31 299 32 300  33 301  34 302  35 303  36 304  37  38 305
>  39306  40 307  41 308  42 309  43 310  44 311  45  73 312  46 313  47 314
>  48 315  49 316  50 317  51 318  52 319 53  74  75  76  77  78  79109 162
>  80 215  81  82 163 110  83 216 164  84 111  85 165  86 217 112  87 166  88
> 218 113  89 167  90 219114  91 168 115  92 220 169  93 116 221  94 117 170
> 222  95 118  96 223 171 119 97 224 172 120 225  98 226 121  99173 227 100
> 122 228 174 101 123 229 102 230 175 124 103 231 176 232 125 104 233 234 105
> 177 126 235 236 106 178 127 237 238 107 239179240 128 241 242 243 180 244
> 129 245 246 247 248 181 249 250 251 130 252 253 254 255 256 257 258 259260
> 261 262

Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

2022-06-21 Thread Benjamin Deck 
External Email - Use Caution

Hi Yujing,

It seems that this did not solve the issue. Are there any other reasons why
this would occur?

Ben

On Fri, Jun 17, 2022 at 2:59 PM Benjamin Deck  wrote:

> Hi Yujing,
>
> Thank you. I will give it a try! Can documentation be updated?
>
> Ben
>
>
> 
>  Virus-free.
> http://secure-web.cisco.com/1XaxW66YQ2SQxo_5UrtvlBYCoJgMWAM-6vHwtRkkgQ1CxFy8po84lfaPBMo1Z4xHtm5tNxN5bdyAzB9Asith1Bt4CwRLFBKKKouRmzKOlY75XrLW-MIJdMjCwjS7sOrYgD90YUEcP3nKiY3UHxldy-kM0YdMw9sxQb2IR75yoM0Lt29riWdrfajhb8pfo71d9d2L99luE43lNSQoAROOdJde8UsoRxBQJqhWPsTAMEEKMAj0BLzkiHb5D595B-JokXhVGP8-CA-8TN2OvMOBIyOarxQBGhfQ92X-_i1qhVfMGqH0nG16ELWjruF48_84l/http%3A%2F%2Fwww.avast.com
> 
> <#m_-6826179491889711689_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
> On Fri, Jun 17, 2022 at 2:56 PM Huang, Yujing 
> wrote:
>
>> Hi Ben,
>>
>>
>>
>> Just wanted to update you on mris_label2annot command line options.
>>
>>
>>
>> If ‘--no-unknown’ is used with mris_label2annot, ‘—offset 1’ should also
>> be specified.
>>
>>
>>
>> Yujing
>>
>>
>>
>> *From:* Huang, Yujing
>> *Sent:* Thursday, June 16, 2022 1:59 PM
>> *To:* Freesurfer support list 
>> *Subject:* RE: [Freesurfer] mri_label2vol fill-ribbon segmentation fault
>>
>>
>>
>> Hi Ben,
>>
>>
>>
>> I’m learning it myself too.
>>
>>
>>
>> I played it a little more.  I see the mismatch can happen if you skip a
>> number in you LUT.
>>
>>
>>
>> Also, if you have ‘0  Unknown 00  0  0’ in your LUT, I’m not
>> sure you should use ‘--no-unknown’ for mris_label2annot. It will cause your
>> annotation off by one.
>>
>>
>>
>> Yujing
>>
>>
>>
>>
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Benjamin Deck
>> *Sent:* Thursday, June 16, 2022 10:58 AM
>> *To:* Freesurfer support list 
>> *Subject:* Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Hi Yujing,
>>
>>
>>
>> Thanks for taking a look. What do you mean by mismatch?
>>
>>
>>
>> The LUT was used to make the annot file. What would generate this
>> mismatch?
>>
>>
>>
>> Here is the output from my mris_label2annot call:
>>
>>
>> mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab
>> sub-DAEK_yeoLUT.txt --ldir
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi lh
>> Reading ctab sub-DAEK_yeoLUT.txt
>> Number of ctab entries 105
>> INFO: no labels specified, generating from ctab
>> mris_label2anno supposed to be reproducible but seed not set
>>  1
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_10_ROIs_1_lh_native.label
>>  2
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_11_ROIs_1_lh_native.label
>>  3
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_1_lh_native.label
>>  4
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_12_ROIs_2_lh_native.label
>>  5
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_1_lh_native.label
>>  6
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_2_lh_native.label
>>  7
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_3_lh_native.label
>>  8
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_4_lh_native.label
>>  9
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_13_ROIs_5_lh_native.label
>> 10
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_1_lh_native.label
>> 11
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_2_lh_native.label
>> 12
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_3_lh_native.label
>> 13
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_4_lh_native.label
>> 14
>> /mnt/

Re: [Freesurfer] mri_aparc2aseg bad incorrect ROIs

2022-06-21 Thread Benjamin Deck 
External Email - Use Caution

 Hi Doug,

Thanks for getting back to me.

Yes, it's very weird. My LUT doesn't contain any subcortical structures but
when I load my custom LUT into Freeview, it shows my surface-based
parcellation in the subcortical regions. Furthermore, my annotation files
look completely fine!

I noticed that the indices of my LUT are the same as the default LUT, could
this be a problem; should my custom LUT have unique index IDs?

For example see the two LUTs:


*FS default LUT:*
#No. Label Name:R   G   B   A

0   Unknown 0   0   0   0
1   Left-Cerebral-Exterior  70  130 180 0
2   Left-Cerebral-White-Matter  245 245 245 0
3   Left-Cerebral-Cortex205 62  78  0
4   Left-Lateral-Ventricle  120 18  134 0
5   Left-Inf-Lat-Vent   196 58  250 0
6   Left-Cerebellum-Exterior0   148 0   0
7   Left-Cerebellum-White-Matter220 248 164 0
.

*My Custom LUT*
0 Unknown 0 0 0 0
1 Net_10_ROIs_1_lh_native 255 255 255 0
2 Net_11_ROIs_1_lh_native 25  5   25  0
3 Net_12_ROIs_1_lh_native 25  100 40  0
4 Net_12_ROIs_2_lh_native 70  130 180 0
5 Net_13_ROIs_1_lh_native 100 100 0   0
6 Net_13_ROIs_2_lh_native 196 58  250 0
7 Net_13_ROIs_3_lh_native 100 25  0   0
.

*Output from the call with your suggestion of --aseg flag:*







































































*mri_aparc2aseg --s sub-DAEK --annot yeo2011 --annot-table
sub-DAEK_yeoLUT.txt --threads 6 --rip-unknown --volmask --aseg
aseg.presurf.hyposSUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjectssubject
sub-DAEKoutvol
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/yeo2011+aseg.mgzuseribbon
0baseoffset 0RipUnknown 18 avail.processors, using 6Reading lh white
surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.whiteReading
lh pial
surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.pialLoading
lh annotations from
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annotHave
color table for lh white annotationRipping vertices labeled as unkownRipped
27062 vertices from left hemiBuilding hash of lh whiteBuilding hash of lh
pialReading rh white
surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.whiteReading
rh pial
surface /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.pialLoading
rh annotations from
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/rh.yeo2011.annotHave
color table for rh white annotationRipping vertices labeled as unkownRipped
27560 vertices from right hemiBuilding hash of rh whiteBuilding hash of rh
pialLoading ribbon segmentation from
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgzLoading aseg
from
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/aseg.presurf.hypos.mgzASeg
Vox2RAS: 0.8   0.0   0.0   127.9; 0.0
0.0   0.8  -127.9; 0.0  -0.8   0.0
127.9; 0.0   0.0   0.0
1.0;-Labeling Slice (320)161 108 214  54   0
267   1  55 268   2 269  56   3 270  57   4 271  58 272   5  59  6 273  60
  7 274  61 275   8  62 276   9  63 277  10  64 278  11  65 279 12  66 280
 67  13 281  68  14 282  15  69 283  16 284  70  17 285  18 286  19287  20
 71 288  21 289  22 290  23 291  24 292  25 293  26 294  27 295  28  72 296
 29 297  30 298  31 299 32 300  33 301  34 302  35 303  36 304  37  38 305
 39306  40 307  41 308  42 309  43 310  44 311  45  73 312  46 313  47 314
 48 315  49 316  50 317  51 318  52 319 53  74  75  76  77  78  79109 162
 80 215  81  82 163 110  83 216 164  84 111  85 165  86 217 112  87 166  88
218 113  89 167  90 219114  91 168 115  92 220 169  93 116 221  94 117 170
222  95 118  96 223 171 119 97 224 172 120 225  98 226 121  99173 227 100
122 228 174 101 123 229 102 230 175 124 103 231 176 232 125 104 233 234 105
177 126 235 236 106 178 127 237 238 107 239179240 128 241 242 243 180 244
129 245 246 247 248 181 249 250 251 130 252 253 254 255 256 257 258 259260
261 262 263 264 265 266 182 183 131 184 185 186 132 187 188 133 189 190 134
191 135 192 193 136 194 137 195 138 196 139197 140 198 141 199142 200 201
143 202 144 203 145 204 205 146 206 147 207 148 208 149 209 150 210 151 211
152 212 153 213 154 155 156 157 158 159160 nctx = 1191735Used brute-force
search on 1567 voxelsWriting output aseg to
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/yeo2011+aseg.mgz#VMPC#
mri_aparc2aseg VmPeak  2534656mri_aparc2aseg done*

Re: [Freesurfer] using brain mask from older FreeSurfer version on a newer

2022-06-21 Thread Douglas N. Greve 
no special flags. 7.2 will update all of the files, it should preserve 
all your edits though


On 6/21/2022 7:21 AM, Aaron Tanenbaum wrote:


External Email - Use Caution

Are there special flags. There are differences between autorecon1 for 
both pipeline. Does 7.2 update some of the files like for instance the 
T1.mgz do to differences in the normalizations.


On Sun, Jun 19, 2022, 3:55 PM Douglas N. Greve 
 wrote:


You should be able to run 7.2 on top of the 5.3 and at will take
all your edits (make a copy of your 5.3 data first:)


On 6/14/2022 5:26 PM, Aaron Tanenbaum wrote:


External Email - Use Caution

Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands
of scans to do.  I see that you can give freesurfer a brainmask.
I was thinking of giving freesurfer a brainmask from the previous
from 5.3 to 7.1. Is this a wise idea? Do you have any objections?

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Re: [Freesurfer] using brain mask from older FreeSurfer version on a newer

2022-06-21 Thread Aaron Tanenbaum 
External Email - Use Caution

Are there special flags. There are differences between autorecon1 for both
pipeline. Does 7.2 update some of the files like for instance the T1.mgz do
to differences in the normalizations.

On Sun, Jun 19, 2022, 3:55 PM Douglas N. Greve 
wrote:

> You should be able to run 7.2 on top of the 5.3 and at will take all your
> edits (make a copy of your 5.3 data first:)
>
>
> On 6/14/2022 5:26 PM, Aaron Tanenbaum wrote:
>
> External Email - Use Caution
> Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans
> to do.  I see that you can give freesurfer a brainmask. I was thinking of
> giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a
> wise idea? Do you have any objections?
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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[Freesurfer] ERROR : mri_ca_register with non-zero status 15

2022-06-21 Thread 김다운 
External Email - Use Caution

Hello FreeSurfer Develops,


I'm attempting to run recon-all on two single subject with T1.

However, I got the following error message for subject respectively:




ERROR : mri_ca_register with non-zero status 15

but continuing despite the error


...


ERROR : cannot find or read transform/talairach.m3z


I have attached the recon-all.log in case it's of any use.

=

my commend code


#!/bin/bash
#SBATCH -N 1 # Number of Nodes required
#SBATCH -c 8 # Number of threads
#SBATCH -t 0-10:00:00 # Amount of time needed DD-HH:MM:SS
#SBATCH -p shared # Partition to submit to
#SBATCH --mem-per-cpu=8GB #Memory per cpu
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
module load freesurfer
export FS_LICENSE=$HOME/license.txt
export SUBJECTS_DIR=~/DWKIM/T1/00sample
recon-all -i s3001.nii -s s3001 -parallel -openmp 8 -all -qcache

==
FreeSurfer Version : freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Platform : CentOS Linux ver.7
uname -a : Linux holylogin04.rc.fas.harvard.edu 3.10.0-1160.36.2.e17.x86_64 #1 
SMP Wed Jul 21 11:57:15 UTC 2021 x86_64 x86 64 x86_64 GNU/Linux

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Re: [Freesurfer] MeanItensities- PET

2022-06-21 Thread Bouchra Guelib 
External Email - Use Caution

Hi,
I want to register PET to T1 MRI using FSL dof12
then I want to extract the SUV.
I would like you to help me on these lines
Firstly I converted my MRI named ADNI.nii T1 to min305 space then I applied
recon-all. The output is the Folder ADNI
Then I want to register my PET to T1 MRI so I use these line
bbregister --s ADNI --init-fsl --t2 --mov PET.nii --reg
Pet2T1.register.dof12.dat --lta Pet2T1.register.dof12.lta --init-reg-out
Pet2T1
here I want to extract SUV so used this commend
mri_segstats --seg ADNI/mri/aparc+aseg.mgz  --sum petsuv.segstats.dat --i
PET.nii  --ctab-default
the CMD displays
ERROR: dimension mismatch between input volume and seg
  input 128 128 90
  seg   256 256 256
Would tell me where is my mistakes


Le dim. 19 juin 2022 à 22:43, Douglas N. Greve  a
écrit :

> You can try removing --default-seg-merge, but it may fail.
> It can compute a relative SUV (relative to a give n ROI). By default, this
> will be pons, but you can chose others. SUV requires knowing things like
> the patients weight.
>
> On 6/19/2022 4:15 PM, Bouchra Guelib wrote:
>
> External Email - Use Caution
> mri_gtmpvc --i ADNI-PET.nii --reg template.reg.lta --psf 6 --seg
> gtmseg.mgz --default-seg-merge  --auto-mask 1 .01 --mgx .01 --o
> gtmpvc.output
> I am trying to do like that.
> I tried to change the --seg gtmseg.mgz by aparc+aseg.mgz to obtain the 45
> subcortical regions but it doesn't work
> PS: does  mri_gtmpvc compute SUV? or the mean intensity?
>
> Le dim. 19 juin 2022 à 20:55, Douglas N. Greve  a
> écrit :
>
>> what is your mri_gtmpvc command line?
>>
>> On 6/19/2022 2:22 PM, Bouchra Guelib wrote:
>>
>> External Email - Use Caution
>> These are the missing regions in which I want to obtain their SUVr.
>> Left-Lateral-Ventricle, Left-Inf-Lat-Vent,
>> 3rd-Ventricle, 4th-Ventricle, Left-vessel,  Right-Lateral-Ventricle, 
>> Right-Inf-Lat-Vent, 5th-Ventricle, WM-hypointensities, 
>> Left-WM-hypointensities,
>> Right-WM-hypointensities, non-WM-hypointensities, 
>> Left-non-WM-hypointensities, Right-non-WM-hypointensities, Optic-Chiasm, 
>> CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior,  CC_Anterior.
>>
>> This is what I get when I apply mri_gtmpvc.
>> I already followed the link that you submitted to me.
>>
>>
>> Le dim. 19 juin 2022 à 15:54, Douglas N. Greve 
>> a écrit :
>>
>>>
>>>
>>> On 6/15/2022 7:40 AM, Bouchra Guelib wrote:
>>>
>>> External Email - Use Caution
>>> Hi,
>>> I wonder if someone can help me to do  something similar to that:
>>> "  the mean intensity of each FreeSurfer region (ROI) for the 45
>>> subcortical and the 68 cortical regions were assessed the mean
>>> intensity of each FreeSurfer region (ROI) for the 45 subcortical and the 68
>>> cortical regions were assessed to obtain  SVU".
>>> Also, I found an article that mentioned that " the estimated total
>>> intracranial volume (eTIV) is calculated, which is used later for
>>> normalization of the volumetric measures".
>>> My questions are:
>>> 1) In "  gtm.stats.dat" not all subcortical regions are mentioned, why?
>>>
>>> which ones are missing?
>>>
>>> 2) I applied "mri_getmpc" to obtain the mean intensity, however, I could
>>> not figure out what I should do after this step to obtain the mean
>>> intensity and compute SVU.
>>>
>>> Do you mean mri_gtmpvc? the values will be in the gtm.stats.dat file
>>>
>>> 3) why do they use eTIV, should I use it, and if yes how!
>>>
>>> I don't know. It does not make sense to correct an intensity with eTIV.
>>> btw, I assume  you've seen this page *MailScanner has detected a
>>> possible fraud attempt from "secure-web.cisco.com" claiming to be*
>>> https://secure-web.cisco.com/10fgLPhblHyLRZyALSM0tAKzNc2G6ixaXzYKhQAoYy_4gCxeIFcHjDNJDh0_0b9RAJpUY3tC2iVevmJcXLbZDp2rOTrLM_ZXD-UZaJKREQRKhy4jwSLFgP5OXiQxr6Fyxjh_Iut61PEpOVtB4y_6bNKRHf63iz9cNLKpr9Xm-kAEioeAva4kSnUb4OQ1cUCS1a6KHPGPMutLN2O4QGGircynJDMcoGkoVP_Gm0Y-xUbIWpxIMuOQa5o0Fe7HiwqBqSK5Z3IP6Tw1iL8zXbNsHk2Ze1C14dtY3v96XmpVMjudyd_AfwPZ8BgqxaGY9ShkHgUVyU4WxfHboYHTKNJQXxQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer
>>> 
>>> ?
>>>
>>> best regards.
>>>
>>>
>>> --
>>> *GUELIB Bouchra: *Ph.D. student
>>> *Lire *Laboratory
>>> University: Constantine 2-Abdelhamid Mehri- *Algeria *
>>> Alternative email: guelibbouc...@gmail.com
>>>
>>>
>>>
>>>
>>>
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