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 <bdeck8...@gmail.com> wrote:

> Hi Yujing,
>
> Thank you. I will give it a try! Can documentation be updated?
>
> Ben
>
>
> <https://secure-web.cisco.com/1CbfxkRGloea4lW2PK478ps9kqnPQiVPiaHMcsD6pnKbPkj_NH1SmVOBOGFDKKPUorKYgfC5qkC_p6LV8AFgUuBb0iAZtOiQkRV4eWc8fjOJiIskZtyGr2DoUb2VTUVyD44esBqpBAOVtbKEkjyhAWPRYookez7RQorpkco895Bn0oLCIhAR9GMINczuWsXNqDvM9YMkv_Ed8JLqBa0qMN6I2T6nRKkKAkq3GSGk6XTUeT0cKoEUp3OGr7rsEQ_-EkqyR92yFtkdFHemStKToaXILJAliBpi46_Tspmq_Yr80fDe684fjbvr-O3WXEAww/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dicon>
>  Virus-free.
> http://secure-web.cisco.com/1XaxW66YQ2SQxo_5UrtvlBYCoJgMWAM-6vHwtRkkgQ1CxFy8po84lfaPBMo1Z4xHtm5tNxN5bdyAzB9Asith1Bt4CwRLFBKKKouRmzKOlY75XrLW-MIJdMjCwjS7sOrYgD90YUEcP3nKiY3UHxldy-kM0YdMw9sxQb2IR75yoM0Lt29riWdrfajhb8pfo71d9d2L99luE43lNSQoAROOdJde8UsoRxBQJqhWPsTAMEEKMAj0BLzkiHb5D595B-JokXhVGP8-CA-8TN2OvMOBIyOarxQBGhfQ92X-_i1qhVfMGqH0nG16ELWjruF48_84l/http%3A%2F%2Fwww.avast.com
> <https://secure-web.cisco.com/1tOZ5nSv06qa69857jrCclTd3YENq-4Gk0R8zTlVZo__kYkxRrdsEohQaleNqig9ySPT09bAtTCifKMf_OwGSTmpZBCPs8i_BM-j6n9OGztiXhaL3NbOU-7rrucIhcyhnA6BGcjTkpg5xg1A9DpzGjcLBaE-sFwlFOicNzIAxs9EwU_FxBtUr0EtPt-ZNnKnSQ41HR59oshUwNWw25ic3M58ch6CIly9Eyyb-rGH4aYxdYsDff9evt04MgfZh67XWnw5tcDW93z9PRPVOggrV7IdO2cs57eHdU6rbOYkauy7krQJMspzouJ7M9wYnCAjd/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dlink>
> <#m_-6826179491889711689_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
> On Fri, Jun 17, 2022 at 2:56 PM Huang, Yujing <yhuan...@mgh.harvard.edu>
> 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 <freesurfer@nmr.mgh.harvard.edu>
>> *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 0    0      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 <freesurfer@nmr.mgh.harvard.edu>
>> *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/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_14_ROIs_5_lh_native.label
>> 15
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_15_ROIs_1_lh_native.label
>> 16
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_1_lh_native.label
>> 17
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_16_ROIs_2_lh_native.label
>> 18
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_1_lh_native.label
>> 19
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_2_lh_native.label
>> 20
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_3_lh_native.label
>> 21
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_17_ROIs_4_lh_native.label
>> 22
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_1_lh_native.label
>> 23
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_2_lh_native.label
>> 24
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_3_lh_native.label
>> 25
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_4_lh_native.label
>> 26
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_18_ROIs_5_lh_native.label
>> 27
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_19_ROIs_1_lh_native.label
>> 28
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_1_lh_native.label
>> 29
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_2_ROIs_2_lh_native.label
>> 30
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_1_lh_native.label
>> 31
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_2_lh_native.label
>> 32
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_3_ROIs_3_lh_native.label
>> 33
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_4_ROIs_1_lh_native.label
>> 34
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_1_lh_native.label
>> 35
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_2_lh_native.label
>> 36
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_3_lh_native.label
>> 37
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_5_ROIs_4_lh_native.label
>> 38
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_1_lh_native.label
>> 39
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_2_lh_native.label
>> 40
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_6_ROIs_3_lh_native.label
>> 41
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_1_lh_native.label
>> 42
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_7_ROIs_2_lh_native.label
>> 43
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_1_lh_native.label
>> 44
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_2_lh_native.label
>> 45
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_3_lh_native.label
>> 46
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_4_lh_native.label
>> 47
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_8_ROIs_5_lh_native.label
>> 48
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_1_lh_native.label
>> 49
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_2_lh_native.label
>> 50
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//lh.Net_9_ROIs_3_lh_native.label
>>
>> 7.2.0
>> cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels
>> cmdline 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
>> sysname  Linux
>> hostname LAPTOP-LPS9CH5E
>> machine  x86_64
>> user     bdeck8317
>>
>> subject sub-DAEK
>> hemi    lh
>> SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects
>> ColorTable sub-DAEK_yeoLUT.txt
>> AnnotName  yeo2011
>> nlables 50
>> LabelThresh 0 0.000000
>> Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.orig
>>  0 1336330 Net_10_ROIs_1_lh_native
>>  1 1639705 Net_11_ROIs_1_lh_native
>>  2 2647065 Net_12_ROIs_1_lh_native
>>  3 11829830 Net_12_ROIs_2_lh_native
>>  4 25700 Net_13_ROIs_1_lh_native
>>  5 16399044 Net_13_ROIs_2_lh_native
>>  6 6500 Net_13_ROIs_3_lh_native
>>  7 3294840 Net_13_ROIs_4_lh_native
>>  8 660700 Net_13_ROIs_5_lh_native
>>  9 6558940 Net_14_ROIs_1_lh_native
>> 10 7874740 Net_14_ROIs_2_lh_native
>> 11 14465658 Net_14_ROIs_3_lh_native
>> 12 9180300 Net_14_ROIs_4_lh_native
>> 13 12300 Net_14_ROIs_5_lh_native
>> 14 9182740 Net_15_ROIs_1_lh_native
>> 15 3296035 Net_16_ROIs_1_lh_native
>> 16 9211105 Net_16_ROIs_2_lh_native
>> 17 4924360 Net_17_ROIs_1_lh_native
>> 18 3302560 Net_17_ROIs_2_lh_native
>> 19 3988500 Net_17_ROIs_3_lh_native
>> 20 3988540 Net_17_ROIs_4_lh_native
>> 21 13777468 Net_18_ROIs_1_lh_native
>> 22 9221340 Net_18_ROIs_2_lh_native
>> 23 3302420 Net_18_ROIs_3_lh_native
>> 24 3294765 Net_18_ROIs_4_lh_native
>> 25 14443610 Net_18_ROIs_5_lh_native
>> 26 10511400 Net_19_ROIs_1_lh_native
>> 27 8323072 Net_2_ROIs_1_lh_native
>> 28 1326300 Net_2_ROIs_2_lh_native
>> 29 3957880 Net_3_ROIs_1_lh_native
>> 30 1316060 Net_3_ROIs_2_lh_native
>> 31 14464220 Net_3_ROIs_3_lh_native
>> 32 8323072 Net_4_ROIs_1_lh_native
>> 33 7874740 Net_5_ROIs_1_lh_native
>> 34 9180300 Net_5_ROIs_2_lh_native
>> 35 8860211 Net_5_ROIs_3_lh_native
>> 36 9182740 Net_5_ROIs_4_lh_native
>> 37 3296035 Net_6_ROIs_1_lh_native
>> 38 9211105 Net_6_ROIs_2_lh_native
>> 39 4924360 Net_6_ROIs_3_lh_native
>> 40 3302560 Net_7_ROIs_1_lh_native
>> 41 3988500 Net_7_ROIs_2_lh_native
>> 42 3988540 Net_8_ROIs_1_lh_native
>> 43 9221340 Net_8_ROIs_2_lh_native
>> 44 3302420 Net_8_ROIs_3_lh_native
>> 45 3302620 Net_8_ROIs_4_lh_native
>> 46 10811612 Net_8_ROIs_5_lh_native
>> 47 2637020 Net_9_ROIs_1_lh_native
>> 48 1326300 Net_9_ROIs_2_lh_native
>> 49 3957880 Net_9_ROIs_3_lh_native
>> Writing annot to
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/lh.yeo2011.annot
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Ben
>>
>>
>>
>> [image: Image removed by sender.]
>> <https://secure-web.cisco.com/1zRfRnNJbztJhB7UFpY-K9ElZkCsAXpOnfc4n5fGn_R5Lv3vYBe-DsvV2hD4RDdJESnYGiwa-L8Usq00gA3vDfDULMiYvXWIzao4-CCFex8VxZnEHyoZHi_w7aOP9zR8Lrr1Y8z3LBtoV6HZW8rn-UKIJUQ6msWLaxB8mg03Gc0PhRJMTE8Qm9XVocf2vYyAJFjmc7lVmM7DazR_v-LV7kBKizsgmbvfoTdGY6GFqZf1ShyhFoJHgc9JeGE4CSemo1hSyhVqXv_Bw__nW7cCDxnOY2v4wavzxDh0mLF-AWtZPFzdq3Yqf7U-O-QMGJJP2/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dicon>
>>
>> Virus-free. *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be* 
>> http://secure-web.cisco.com/1XaxW66YQ2SQxo_5UrtvlBYCoJgMWAM-6vHwtRkkgQ1CxFy8po84lfaPBMo1Z4xHtm5tNxN5bdyAzB9Asith1Bt4CwRLFBKKKouRmzKOlY75XrLW-MIJdMjCwjS7sOrYgD90YUEcP3nKiY3UHxldy-kM0YdMw9sxQb2IR75yoM0Lt29riWdrfajhb8pfo71d9d2L99luE43lNSQoAROOdJde8UsoRxBQJqhWPsTAMEEKMAj0BLzkiHb5D595B-JokXhVGP8-CA-8TN2OvMOBIyOarxQBGhfQ92X-_i1qhVfMGqH0nG16ELWjruF48_84l/http%3A%2F%2Fwww.avast.com
>> <https://secure-web.cisco.com/1f-mu2Bhnd8i3u9-0Rrkb9wcQs3dpO6ZBXI3wMPsujw2ZJK7q1QiklKYc5v4PhKLfQ0z4dDi4l2bvV044-uH_3p1QKpj0FuhVHGMGmNqlk5yFHVP8S0B1kLbNAyfebWz_FxsbqzvVHe_Eru_OI49E4lYddCw6L56VTcN-ZLd2GctbSCGAo6IcTE3J4e435EfVAK9-Ej29Ps0QkdiQeAWKUJGG4pq_8g32ctjKz8yOQCIAHpTNyeN1F8nvA5ERYFLzYxK4wxHp9_r8CbXNJA0Brqw7JQkXt9yeMv4ypyYq30ft5Wd32XC5GCHOLcYmb4vq/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dlink>
>>
>>
>>
>> On Tue, Jun 14, 2022 at 1:33 PM Huang, Yujing <yhuan...@mgh.harvard.edu>
>> wrote:
>>
>> Hi Ben,
>>
>>
>>
>> I was able to reproduce the core dump.  In my case, it was because a
>> mismatch of color scheme between input annotation file and the color table
>> loaded with the surface.
>>
>>
>>
>> I suspect it might be the same issue for you too. But I’m not sure what
>> the right action is to work around this.
>>
>>
>>
>> Yujing
>>
>>
>>
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Benjamin Deck
>> *Sent:* Friday, June 10, 2022 11:47 AM
>> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> *Subject:* [Freesurfer] mri_label2vol fill-ribbon segmentation fault
>>
>>
>>
>> *        External Email - Use Caution        *
>>
>> Hi there,
>>
>>
>>
>> Having issues with the following command:
>>
>>
>>
>> mri_label2vol --annot lh.yeo_2011.annot --temp
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz  --hemi lh
>> --fill-ribbon --identity --subject sub-DAEK --o lh.sub-DAEK_annot_nat.nii.gz
>>
>>
>>
>>
>>
>> produces the following error:
>>
>>
>>
>> Number of labels: 0
>> Annot File:      lh.yeo_2011.annot
>> Template Volume:
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz
>> Outut Volume: lh.sub-DAEK_annot_nat.nii.gz
>> Registration File: (null)
>> Fill Threshold: 0
>> Label Vox Vol:  1
>> ProjType:       (null)
>> ProjTypeId:     0
>> ProjStart:      0
>> ProjStop:       0
>> ProjDelta:      0.1
>> Subject:  sub-DAEK
>> Hemi:     lh
>> UseNewASeg2Vol:  0
>> DoLabelStatVol  0
>> LabelCodeOffset  0
>> setenv SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects
>> 7.2.0
>> Template RAS-to-Vox: --------
>> -1.25000  -0.00000  -0.00000   160.00000;
>> -0.00000  -0.00000  -1.25000   160.00000;
>> -0.00000   1.25000  -0.00000   160.00000;
>> -0.00000  -0.00000  -0.00000   1.00000;
>> Template Voxel Volume: 0.512
>> nHits Thresh: 0
>> Using Identity Matrix
>> RegMat: --------
>>  1.00000   0.00000   0.00000   0.00000;
>>  0.00000   1.00000   0.00000   0.00000;
>>  0.00000   0.00000   1.00000   0.00000;
>>  0.00000   0.00000   0.00000   1.00000;
>> Label RAS-to-Vox: --------
>> -1.25000   0.00000   0.00000   160.00000;
>>  0.00000   0.00000  -1.25000   160.00000;
>>  0.00000   1.25000   0.00000   160.00000;
>>  0.00000   0.00000   0.00000   1.00000;
>>   INFO: loading surface
>>  /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.white
>> nvertices = 253237
>> Reading thickness
>> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/lh.thickness
>> Loading annotations from lh.yeo_2011.annot
>> annotidmax = 48
>> nlabels = 48
>> Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/ribbon.mgz
>> Mapping
>> Segmentation fault
>>
>>
>>
>>
>>
>> But when I run the same command without fill-ribbon the process runs to
>> completion.
>>
>>
>>
>> Not sure if this is a memory issue or something else.
>>
>>
>>
>> Ben
>>
>>
>> --
>>
>> *Benjamin L. Deck*
>>
>> *Doctoral Student*
>>
>> *Applied Cognitive and Brain Sciences*
>>
>> *Department of Psychological and Brain Sciences*
>>
>> *Drexel University*
>>
>>
>>
>> [image: Image removed by sender.]
>> <https://secure-web.cisco.com/1iKwJbETCAUSlHWE3gbz9IWJ4YvkeL0JhP2fGTP_IRLe0YAuJSsGlpOrQHNVfjuiKYqhmSgH5KSYV_gD6T-ANkaBo1hZWN5AQcHGQwryr0EDsu8NqPcxBZV72UfiPAjYeGdUOFXa8ZAiJxtxf0Q72lp00VpPQNLMHYmAkpu-T-1lhDuMYW579S_wn2oo0a0NYH3gCT_0nvVAgRq9VgIDidx0P2oUyENgIAM6sjaEuUnHLfBrU9x9ZKZbmgbb7zcIjaVn8naws7kOTAcRCm7m_HwRuicAaOxXjHM2dP8MTOhvy94l9zWgewN3dP4a3gLUE/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dicon>
>>
>> Virus-free. *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be* 
>> http://secure-web.cisco.com/1XaxW66YQ2SQxo_5UrtvlBYCoJgMWAM-6vHwtRkkgQ1CxFy8po84lfaPBMo1Z4xHtm5tNxN5bdyAzB9Asith1Bt4CwRLFBKKKouRmzKOlY75XrLW-MIJdMjCwjS7sOrYgD90YUEcP3nKiY3UHxldy-kM0YdMw9sxQb2IR75yoM0Lt29riWdrfajhb8pfo71d9d2L99luE43lNSQoAROOdJde8UsoRxBQJqhWPsTAMEEKMAj0BLzkiHb5D595B-JokXhVGP8-CA-8TN2OvMOBIyOarxQBGhfQ92X-_i1qhVfMGqH0nG16ELWjruF48_84l/http%3A%2F%2Fwww.avast.com
>> <https://secure-web.cisco.com/1lKwnHJD_3HKNZFq3yBeIxnL1wagOdiYUAdM7xFJLwCTPpWOVxKWfJ_INP6ff3NFDguVU8luyEeB0A_eghbJamJYyDSqV_tvIuNd4MOeGl-FJ1e1Q9h2qfNbONRZmDV88ErPsp3n0dMRCaqJsc3f5gC-yphrEBAq-GC_SI3CxBaBk5RpBMVLxReS5GbzJElOPa8nn81TTTMegPgBS-Gz8Vdq8vzeEoOgzzgWLqaKINJJtoe8TxBUfvIeTXwxCpEoDmkosL38-remOhJy78-FIS0GfZhAAeMG0rVHnSjxyKafzJNYA-z85paoXHDhg-OyE/https%3A%2F%2Fwww.avast.com%2Fsig-email%3Futm_medium%3Demail%26utm_source%3Dlink%26utm_campaign%3Dsig-email%26utm_content%3Dwebmail%26utm_term%3Dlink>
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1KFYgeucywv-sgvlszrUVmMExT1D1wTosDU5A-ke32OnzTiJE16BPNnIWUUrRFHCfQlcwzvjB9Q_K1vkrSEJCUQDTLqRHU2UEQjr1vhUytcvG7hKX9glUJjoxbSUY8O_1bQYvpZ7TOKLJ9YXI87fsdsCjOCH8pB3fiIxiezlWu0z6nZe6wVVSJFDrDdBem0x4EW9r5DDygdavp_pb5Y0W7eDFR-iX1WCGnPMNjDjpXexXTIdI_Ol2eLqKWFGHW4MUrUqdaqwYDldwTkGvUFz36lUI7bBBSR8z1QvvqnzPopmvsUdYFcp1-fYYTK9hnrhV/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> <https://secure-web.cisco.com/1FUT55eeYf35M-JkMc7UcSX6tQwoolQhFqBp-8LICAUTK0wswJKgW_N0VLBuD8TraBJXxv3A6xEtjOi3zHO6u6hS8qtjCvZLT8blEvNFm05eSJH6b8e3aKqHBqbtFAVOULtn9jgTodt8mPW8m3GmSRUmYpxpu9C3Fkzsso7QpJnn8ogCvZ1glcbo1qzY7f0tbdno7w-kyEgSnfbCNbMMoMyfrKVBy_uY9PmTLYP1fcwc9XbQsn81kFW3GvhlFpwBGRN3Le_la1zqvtr5WRJXwA7glAv3TYsHu2WOT_uygJjXNbYUcMNoxCuIb_tjOc9SD/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
>> The information in this e-mail is intended only for the person to whom it
>> is addressed.  If you believe this e-mail was sent to you in error and the
>> e-mail contains patient information, please contact the Mass General
>> Brigham Compliance HelpLine at *MailScanner has detected a possible
>> fraud attempt from "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1KBqYHmYqf-cm-adopQpa1hFDYwc2XxJdOhqXuwG4-p6H_zGJt9CzUb5Bcvty-89vJmkrh4_Y832uL8-DrSaORXDjxvEkwEs8RtxEuQq6lUEUmTfDzlsSL76rkunUEu1FsCKZ4XZ2Wo3E5uXvAb9ZbgagP66-F2BJ-VUqW_2K-K6ArkhyxeOBbFK_7nQsQrvVhi-lxaWl99ahxDwxvyDw0a4G2bKYecYvPx4JDXZOIqOnUJXhrMxb6r-ORsKccILBkvac-C0TUvVDohtWjtbk5SAJgnuIecC_IkYNBNjmdIGPIAtOk50-zSkafZunnfTb/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>> <https://secure-web.cisco.com/129Kw4R0yoVeTC6bBd1uPUqKUYuQfV-mbD5MR0g-xyo9r99gu2Z-4tY7718A6CVUVsK1u7S1awCDro02sozDsoDFvIHYrhSD5vMlHw_EqisjHZyR11ZdEG2yXwgzu8-sfddrPtz3WvbkujxTvALD-PjFOcUYI_NvZuv-09oniwNIjtKWtpQ32jhSYbp70bpRYQbXH0r71ZqTKS8pYf708p8tjI23a7uEnlutWE573EHFSyZ96N8DYzjiawb99BHqVBLAHIt9CDL5wOEykkXYkYd_eyC6CASQ3k0otyq32qfMyZs0UoWTGjs1OtVTWvtUe/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>> <*MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1KBqYHmYqf-cm-adopQpa1hFDYwc2XxJdOhqXuwG4-p6H_zGJt9CzUb5Bcvty-89vJmkrh4_Y832uL8-DrSaORXDjxvEkwEs8RtxEuQq6lUEUmTfDzlsSL76rkunUEu1FsCKZ4XZ2Wo3E5uXvAb9ZbgagP66-F2BJ-VUqW_2K-K6ArkhyxeOBbFK_7nQsQrvVhi-lxaWl99ahxDwxvyDw0a4G2bKYecYvPx4JDXZOIqOnUJXhrMxb6r-ORsKccILBkvac-C0TUvVDohtWjtbk5SAJgnuIecC_IkYNBNjmdIGPIAtOk50-zSkafZunnfTb/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>> <https://secure-web.cisco.com/129Kw4R0yoVeTC6bBd1uPUqKUYuQfV-mbD5MR0g-xyo9r99gu2Z-4tY7718A6CVUVsK1u7S1awCDro02sozDsoDFvIHYrhSD5vMlHw_EqisjHZyR11ZdEG2yXwgzu8-sfddrPtz3WvbkujxTvALD-PjFOcUYI_NvZuv-09oniwNIjtKWtpQ32jhSYbp70bpRYQbXH0r71ZqTKS8pYf708p8tjI23a7uEnlutWE573EHFSyZ96N8DYzjiawb99BHqVBLAHIt9CDL5wOEykkXYkYd_eyC6CASQ3k0otyq32qfMyZs0UoWTGjs1OtVTWvtUe/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>>
>> .
>> Please note that this e-mail is not secure (encrypted).  If you do not
>> wish to continue communication over unencrypted e-mail, please notify the
>> sender of this message immediately.  Continuing to send or respond to
>> e-mail after receiving this message means you understand and accept this
>> risk and wish to continue to communicate over unencrypted e-mail.
>>
>>
>>
>> --
>>
>> *Benjamin L. Deck*
>>
>> *Doctoral Student*
>>
>> *Applied Cognitive and Brain Sciences*
>>
>> *Department of Psychological and Brain Sciences*
>>
>> *Drexel University*
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://secure-web.cisco.com/1KFYgeucywv-sgvlszrUVmMExT1D1wTosDU5A-ke32OnzTiJE16BPNnIWUUrRFHCfQlcwzvjB9Q_K1vkrSEJCUQDTLqRHU2UEQjr1vhUytcvG7hKX9glUJjoxbSUY8O_1bQYvpZ7TOKLJ9YXI87fsdsCjOCH8pB3fiIxiezlWu0z6nZe6wVVSJFDrDdBem0x4EW9r5DDygdavp_pb5Y0W7eDFR-iX1WCGnPMNjDjpXexXTIdI_Ol2eLqKWFGHW4MUrUqdaqwYDldwTkGvUFz36lUI7bBBSR8z1QvvqnzPopmvsUdYFcp1-fYYTK9hnrhV/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> The information in this e-mail is intended only for the person to whom it
>> is addressed.  If you believe this e-mail was sent to you in error and the
>> e-mail contains patient information, please contact the Mass General
>> Brigham Compliance HelpLine at
>> https://secure-web.cisco.com/1KBqYHmYqf-cm-adopQpa1hFDYwc2XxJdOhqXuwG4-p6H_zGJt9CzUb5Bcvty-89vJmkrh4_Y832uL8-DrSaORXDjxvEkwEs8RtxEuQq6lUEUmTfDzlsSL76rkunUEu1FsCKZ4XZ2Wo3E5uXvAb9ZbgagP66-F2BJ-VUqW_2K-K6ArkhyxeOBbFK_7nQsQrvVhi-lxaWl99ahxDwxvyDw0a4G2bKYecYvPx4JDXZOIqOnUJXhrMxb6r-ORsKccILBkvac-C0TUvVDohtWjtbk5SAJgnuIecC_IkYNBNjmdIGPIAtOk50-zSkafZunnfTb/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>>  <
>> https://secure-web.cisco.com/1KBqYHmYqf-cm-adopQpa1hFDYwc2XxJdOhqXuwG4-p6H_zGJt9CzUb5Bcvty-89vJmkrh4_Y832uL8-DrSaORXDjxvEkwEs8RtxEuQq6lUEUmTfDzlsSL76rkunUEu1FsCKZ4XZ2Wo3E5uXvAb9ZbgagP66-F2BJ-VUqW_2K-K6ArkhyxeOBbFK_7nQsQrvVhi-lxaWl99ahxDwxvyDw0a4G2bKYecYvPx4JDXZOIqOnUJXhrMxb6r-ORsKccILBkvac-C0TUvVDohtWjtbk5SAJgnuIecC_IkYNBNjmdIGPIAtOk50-zSkafZunnfTb/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>>  .
>> Please note that this e-mail is not secure (encrypted).  If you do not
>> wish to continue communication over unencrypted e-mail, please notify the
>> sender of this message immediately.  Continuing to send or respond to
>> e-mail after receiving this message means you understand and accept this
>> risk and wish to continue to communicate over unencrypted e-mail.
>>
>
>
> --
> *Benjamin L. Deck*
> *Doctoral Student*
> *Applied Cognitive and Brain Sciences*
> *Department of Psychological and Brain Sciences*
> *Drexel University*
>


-- 
*Benjamin L. Deck*
*Doctoral Student*
*Applied Cognitive and Brain Sciences*
*Department of Psychological and Brain Sciences*
*Drexel University*
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Reply via email to