Hi Harriet

Do you know that it is a hole? More likely is that it only looks like one on a single slice and if you scroll back and forth or change to a different view you will find that it is not actually a hole.

As for the second question you only need to edit things if the nearby surfaces are in cortex and not accurate. If they are not accurate in the ventricles but fine in cortex it won't change any cortical results.

Cheers
Bruce

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Harriet Cornwell
Sent: Wednesday, November 11, 2020 5:37 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Editing Issues

        External Email - Use Caution        

Hi Jocelyn,

Many thanks for your response. I just wanted to confirm a couple of things:

1. Could you advise what specific edits need to be made to the brainmask.mgz volume to fix the hole in the WM, i.e., do we need to add GM, delete GM? We are used to only editing the brainmask.mgz volume when there is an issue with the GM so just want to make sure that we are fixing this hole in the WM correctly.
2. If we are only interested in cortical thickness, surface area, volume and gyrification, can you confirm that we do not need to spend time editing issues around the ventricles?

Thank you in advance.

Harriet
PhD Student | University of Bath

-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of freesurfer-request@nmr.mgh.harvard.edu
Sent: 10 November 2020 17:00
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 201, Issue 15

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Today's Topics:

   1. BIDS-ASL request for comments - closes THIS Friday        (11/13)
      {Disarmed} (Franklin Feingold)
   2. Re: Editing Issues (Mora, Jocelyn S.)
   3. Create new .mgz from .annot (Hyon, Justin J.)
   4. eddy_correct with DTI {Disarmed} (Wei Shao)
   5. Correlation between thickness and csf_measures: vector
      (Steve Petersen)
   6. color and sign of sig.mgh data (Rovai Antonin)
   7. Postdoctoral Fellowship in advanced multi-parametric imaging
      in Parkinson?s disease, Alzheimer?s disease, and healthy aging
      (Maurizio Bergamino)
   8. Re: Freesurfer 7.1.0 on CentOS 8.1 {Disarmed} (Snedden, Ali)
   9. Re: trac-all -bedp error after successful -prep (Michele Valotti)
  10. Re: Help with mergecontrasts-sess function (Paula Maldonado)

----------------------------------------------------------------------

Message: 1
Date: Mon, 9 Nov 2020 18:28:16 +0000
From: Franklin Feingold <ffein@stanford.edu>
Subject: [Freesurfer] BIDS-ASL request for comments - closes THIS
        Friday  (11/13) {Disarmed}
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <FA8577FC-D779-46BC-927D-79E95EE1BFEE@stanford.edu>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution

The BIDS community is preparing to merge the ASL (Arterial Spin Labeling) extension. The updated draft is available for review at: https://secure-web.cisco.com/1ITF4bOtJJcQiVKXDz67qOkjGMsukmz9eyHDd76OIYTeEMNhcr-pqzFItqXqpDSSs15cEGSM-LrPij2uIMXaEUhiYM9VBUWlYHpl6CKp6ecnNL4nu6GxSu3B8ygb9a_NDvB6BrFIj_IjRi6Cs3Mx7WEkzrp1lreTbNG4d0dAIIai8uDUzrPdnbi3hvAu-RA3uranehnaBDwDX5YZPHc2h-JRIAht_14FygxKNlfjB34u2xmrgzL0_kqWzJs3Jue_Q2zA8ETOI13z51HTkNEjhDA/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F19iI4s--bs7Y_Tdzvgf_eO4rOWt7fabvAARvcNytKJYcOiFI6gGONKUG4ASQvypqsJms2A8I_a2oiLM9epfyjdHtyXW6CaNjs-zFsB_dB6GOFCZjkphCKIXh58QzBtMdlVxRojSk3ksyJJ0amn1AAmltb56n3xoeIneV_uYbxiR-mQaA9pzH2ocGhCflORlUq0kaNtEPAGgtsQXz111gtqA%252Fhttps%25253A%25252F%25252Fbids-specification--652.org.readthedocs.build%25252Fen%25252F652%25252F04-modality-specific-files%25252F01-magnetic-resonance-imaging-data.html%252523arterial-spin-labeling-perfusion-data%26data%3D04%257
 C01%257Chgc36%2540bath.ac.uk%257C2d139b3addcf46cf338308d8859a5ceb%257C377e3d224ea1422db0ad8fcc89406b9e%257C0%257C0%257C637406245354469411%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DYqxPzs0rQWIBMZM3J7yUa7%252BOWHbg7L3F4pC7qj6Pg%252BM%253D%26reserved%3D0, and comments and suggestions may be submitted on GitHub at: https://secure-web.cisco.com/1VL_oxffggPudlMHXkbtyOToPXYFpi9_8kZMHoiuC326KyVVM46BPucmgXBhCMo0ZWZ_GO5h_zABLt6-6L-lz63SdUJyQH4J7k-aGlDAgS3wemkV2woUCoBeJMz3ie10n2pmxmKK_p7zoqvJuHKQAfXgj3efnN5tq9qz-RGvm_QoXwbiHzbD0jyp3W8X_xgD4eT4lK6fYEki0ZQ2T-QSclr3EbuFplrcma8b6zCNljq7s6NPv7d7AfBH4uhH3c3LLfaZTM5fPA8zob9jMLNOVBQ/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1e1-qVFLFl7Vo9V2lZkAqUWA79qa_CZHfymhuxcQvkG9OahetuQhti5mRNs3fI4XCNl00pT4ocbt0U-ovp3zM0uD6zBtJM5aThGTfU8rgXiAaUnAyTObri4Eh_Idgb6oEHWGJpb4-FlBpTvZ4J5zXCQzzFER4BNxuiOodRiiDtQsV0Uqn8Q5HEu6cwue8U8D
 mfyD04TBeqzZeF3EZfNF8Lw%252Fhttps%25253A%252!
 52F%2525
2Fgithub.com%25252Fbids-standard%25252Fbids-specification%25252Fpull%25252F652%26data%3D04%257C01%257Chgc36%2540bath.ac.uk%257C2d139b3addcf46cf338308d8859a5ceb%257C377e3d224ea1422db0ad8fcc89406b9e%257C0%257C0%257C637406245354469411%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DLDzJVrSYyfuH%252BTMB7kaCrGCZ1JouNwQS7unzGUsEGm4%253D%26reserved%3D0. The community review will close on Friday (Nov 13) at 11:5
 9pm PT (pacific time)

This BIDS extension seeks to establish how ASL data and additional metadata are organized within the BIDS structure. This encompasses the ASL sequences provided in the consensus paper [Alsop 2014], including single- and multi-time point pulsed and (pseudo)-continuous ASL.

The final review entails a two week period for public commenting, with a possibility of extension for unresolved discussion. Once public comments are concluded, there will be a one week freeze, during which only critical issues will be considered. (For more details on the release protocol, see https://secure-web.cisco.com/1A8qnp7KY-M8xxjfEiWTabhYuW0g9mTh5DrlGyQ6pc4EAySHTOG3w3y4L57Ctq0sWKr08ZogOHKdp1Bfv0Y4bihJvfACv0J9M3ejly5UWFgGz3Iy7O7ipOuCwaGWAsRt8A5W3FRGBu0TGHfo2vZBoY5gA6Ja3mQs1ydcMxj_x4K38qp_zliaC4xea_hd2lmsPHxiVCYQaBtB_YfJPG0XjGsGtiM_oiJOV-DIo07oynkjieO2s_F5ktN_99EQhJdq3_GQIyz32GS0PtG1HIaD73w/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F18WQObGNOBtv6TPfRTvCtrEQv4TE4obqTEzfsuYxPZfeIyFZ1VzLppLkIzVdd0dE5ifMy0KS_NalQuGW_sfnIOBnPrAeVY2JSlAxNyQQlA7B0pUjy-JAq3e1KcT7PR0lhenu1jqSlP6b9DgHpCvLsOGnGq885qi1l_5OyXWoJgab_2b-XgBTpqKFHCS0NYXqYlohILs7SUWyFPbO94Ixp8Q%252Fhttps%25253A%25252F%25252Fgithub.com%25252Fbids-standard%25252Fbi
 ds-specification%25252Fblob%25252Fmaster%25252FRelease_Protocol.md%26data%3D04%257C01%257Chgc36%2540bath.ac.uk%257C2d139b3addcf46cf338308d8859a5ceb%257C377e3d224ea1422db0ad8fcc89406b9e%257C0%257C0%257C637406245354469411%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DdeGJPrmEZ8dzKduNS2wRSBR4kpWDTrLl4PU96r8x6MA%253D%26reserved%3D0)

We look forward to hearing your feedback!

The BIDS Team

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------------------------------

Message: 2
Date: Mon, 9 Nov 2020 20:54:00 +0000
From: "Mora, Jocelyn S." <JSMORA@mgh.harvard.edu>
Subject: Re: [Freesurfer] Editing Issues
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <DM6PR04MB530883D92F058049E29892AA9EEA0@DM6PR04MB5308.namprd04.prod.outlook.com>

Content-Type: text/plain; charset="us-ascii"

Hi Harriet,

Regarding the first screenshot - If the hole is apparent in more than one or two slides, appears in the 3D window, and could be significant to your study, I would recommend manually editing the brainmask.mgz volume.

With regards to the second screenshot - FreeSurfer measures cortical surfaces so it is typical for non-cortical areas, such as around ventricles and the hippocampus, to appear that there are areas unaccounted for. This is not an error. It is possible, however, to edit the segmentation if you are interested.

For more information on FreeSurfer output and how and when to make edits, you can refer to our tutorial wiki pages for further instruction:
https://secure-web.cisco.com/1QHlhu3xWtQmnfAapeZ10h9EbAQtulPB84RznGqSm73oNLpPyNmfYJSG795r05QJsP9K-T4pNqaKCvI7mTYszDGQ6yPNznOTpyU7aQrrTzkeNfVDhmk4meQXIqY_3rdRdRYNMVcj8w2aPC_PhJ0MpXU8uZi5FCHNE5BAAW14LITSuNCUrRxCYiaaDyOYIatPHFfkNu-Ezx7zyya3uuolWBRmPN8VogXQ0sSuLLUnJYFFQDF45IjgfnPCMRSxRWfWQ1PNwNgDowYqtR1Pu1i38Zg/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Ffswiki%252FFsTutorial%252FOutputData_freeview%26data%3D04%257C01%257Chgc36%2540bath.ac.uk%257C2d139b3addcf46cf338308d8859a5ceb%257C377e3d224ea1422db0ad8fcc89406b9e%257C0%257C0%257C637406245354469411%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DCf%252FxdP0vsUC4WjCOaBIQUK5QrHFA1y3D4JsdEGTutjE%253D%26reserved%3D0
https://secure-web.cisco.com/1WquAo7Am2e1Q89T1xAVSek0-CWajR52FTURwhUxCL-heZMvwKhf9H0rY-qr_fE5hOzHohUzRaQSJMEs3mD4DxWrlcbxPttoJTMfIwZjnfw4jjRR8ROFOX_2yIOePCSPEN4vW1XZ8-8qULoi3RpG2XUEc8bxIW_4NymgXh_TZnQjZwP_7-PxFT2VuHlId7IBS5lXIc5LFLkpQHjwfqd_7PZDwGzzBQzAPxhATTLoql3mmto9pjXCpez-KbAx5Thzsz_7jKxq2pP2VhuNNNxS__g/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsurfer.nmr.mgh.harvard.edu%252Ffswiki%252FFsTutorial%252FTroubleshootingDataV6.0%2523Fixingerrors%26data%3D04%257C01%257Chgc36%2540bath.ac.uk%257C2d139b3addcf46cf338308d8859a5ceb%257C377e3d224ea1422db0ad8fcc89406b9e%257C0%257C0%257C637406245354469411%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3D22x7NB72%252Bhl8fyA7L6PJKuo6pZJ7VXTrm7EEpAW%252Bmpc%253D%26reserved%3D0

Best,
Jocelyn

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Harriet Cornwell <hgc36@bath.ac.uk>
Sent: Monday, November 9, 2020 11:55 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Editing Issues

        External Email - Use Caution

Hi FreeSurfer team,

Here are the details regarding the versions of FreeSurfer that my team are using: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

I have a couple of questions regarding editing.

  1.  Whilst editing one brain we discovered a small hole (see just above the cursor on Screenshot 1). Does this require any manual editing? If so, what would you recommend we do?
  2.  We are working with brains that were scanned at multiple sites. FreeSurfer seems to have a problem segmenting around the ventricles (see Screenshot 2) with a number of brains from one of the sites. Is this an issue that requires manual editing and if so, what do you recommend we do?

If you need any further information, please let me know. Thank you in advance for any advice you can offer.

Harriet

PhD Student | University of Bath

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------------------------------

Message: 3
Date: Mon, 9 Nov 2020 20:58:14 +0000
From: "Hyon, Justin J." <jhyon@caltech.edu>
Subject: [Freesurfer] Create new .mgz from .annot
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <A3F81F3C-95A3-4FA5-9981-F6B205BECED9@caltech.edu>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution

Hello,

I?m new to Freesurfer and am trying to learn the steps to manually label some brain regions for use in source localization in MNE. So far my understanding is that I have to create label files which contain the list of coordinates for the vertices in each region, and a color lookup table which has a list of these labels and their corresponding RGB values for display. However, there are a few pieces missing in my understanding. How would I create the label files for each brain region? For example, if I wish to combine several regions found in the Desikan-Killiany atlas, how would I get from the label files generated via ?h.aparc.annot to new label files combining several labels? Also, in order to create a source space in MNE I need a single segmented .mgz output such as aparc.a2009s+aseg.mgz. If I create a new .annot based on my new label files and lookup table, how would I obtain this volume?

Thank You!

------------------------------

Message: 4
Date: Tue, 10 Nov 2020 00:19:10 -0500
From: Wei Shao <wshao@research.baycrest.org>
Subject: [Freesurfer] eddy_correct with DTI {Disarmed}
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <CAOr1y_S1YeUO-UvUkiE4eKKNXy2ZXRc2wEHxg-cmoLqyT-C6=Q@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution

Hi, Freesurfer team,

My name is Weishao, Here is a problem that bothers me a lot I try to run
DTI. I have loaded the FSL module and use the most recent version of
Freesurfer. it's appreciated if someone can help. Thanks.

Here is the script.

dt_recon --b sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bval
sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bvec
--i sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz
--s /home/weishao/scratch/rawdata/sub-AVP6176/
--o /home/weishao/scratch/rawdata/sub-AVP6176/

Here is feedback

-rw-r----- 1 weishao weishao 49041968 Sep  9 11:41
/scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz
INFO: SUBJECTS_DIR is
/project/6019291/shared/software/2017/Core/freesurfer/7.1.0/subjects
dt_recon logfile
Tue Oct 27 16:19:28 EDT 2020
VERSION dt_recon 7.1.0
setenv SUBJECTS_DIR
/project/6019291/shared/software/2017/Core/freesurfer/7.1.0/subjects
cd /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi
/project/6019291/shared/software/2017/Core/freesurfer/7.1.0/bin/dt_recon
--b sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bval
sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bvec --i
sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz --s
/home/weishao/scratch/rawdata/sub-AVP6176/ --o
/home/weishao/scratch/rawdata/sub-AVP6176/
gra95
weishao
/cvmfs/
soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct
ECRefTP 0
#@#-------------------------------
Converting input
Tue Oct 27 16:19:28 EDT 2020
cd /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi
mri_convert
/scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz
/scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz
mri_convert
/scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz
/scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz
reading from
/scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz...
TR=4000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999608, 0.017447, -0.021891)
j_ras = (0.0104682, 0.958258, 0.285714)
k_ras = (-0.0259621, -0.285373, 0.958065)
writing to /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz...

#@#-------------------------------
Eddy/Motion Correct
Tue Oct 27 16:19:44 EDT 2020
cd /scratch/weishao/rawdata/sub-AVP6176/ectmp
eddy_correct /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz
/scratch/weishao/rawdata/sub-AVP6176/dwi-ec.nii.gz 0
/cvmfs/
soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct:
line 95: /cvmfs/
soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/imglob
: *No such file or directory*

Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in
seconds]
     -t : concatenate images in time
     -x : concatenate images in the x direction
     -y : concatenate images in the y direction
     -z : concatenate images in the z direction
     -a : auto-choose: single slices -> volume, volumes -> 4D (time series)
     -tr : concatenate images in time and set the output image tr to the
final option value

*ERROR: when running eddy_correct*

Best,
Wei
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------------------------------

Message: 5
Date: Tue, 10 Nov 2020 11:36:34 +0100
From: Steve Petersen <marfneuro@gmail.com>
Subject: [Freesurfer] Correlation between thickness and csf_measures:
        vector
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <CA+MNVt5NuBAamja44kdyfJ18rzZg_wqow06Dr-v4qBaTf+GLAQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution

Dear Freesurfer experts,

I am conducting a cortical thickness study in three groups. After
performing the between-group analyses, I would like to evaluate the
possible correlation between cortical thickness and the levels of some csf
measures. To do this I included one column in the FSGD file

GroupDescriptorFile 1
Title OSGM
Class N
Class AD_PREC
Class AD_PLUS
Variables CSF_A_measure
Input 4048 N 1730.00
Input 4102 N 2217.00
Input 4122 PREC 652.00
Input 4146 PREC 695.00
Input 4198 PREC 938.00
Input 5049 AD_PLUS 909.00
Input 5080 AD_PLUS 987.00
Input 5096 AD_PLUS 942.00
Input 5101 AD_PLUS 881.00
Input 5232 AD_PLUS 715.00
And so on....

In order to test the possible positive relation between the CSF_A_measure
and the cortical thickness, that is, *does the correlation between
thickness and csf_A_measure differ from zero?, *I would use the following
vector and commands for the left hemisphere.

*Question 1.* Please, can you verify if this vector and commands are
correct.

correlation_vector.mtx -----> 0 0 0 1 1 1

mris_preproc --fsgd J3.fsgd \
  --cache-in thickness.fwhm10.fsaverage \
  --target fsaverage \
  --hemi lh \
  --out lh_J3G_thickness.10.mgh \

mri_glmfit \
--y lh_J3G_thickness.10.mgh \
--fsgd J3.fsgd \
--C correlation_vector.mtx \
--surf fsaverage lh \
--cortex \
--glmdir 01_lh_thickness_results\

mri_glmfit-sim \
  --glmdir 01_lh_thickness_results \
  --sim mc-z 10000 2.3 mc-z.pos \
  --sim-sign pos --cwpvalthresh 0.05\
  --2spaces --overwrite \

*Question 2:* I tried to run these commands with the permutation method but
the terminal gave to me a warning message saying that the matrix is not
orthogonal and if I really want to run the analysis I should add the
--perm-force argument, in this case should I use other method or can I use
the --perm-force safetely?.

Thank you very much for your help in advance.

Best regards,

Steve,
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------------------------------

Message: 6
Date: Tue, 10 Nov 2020 13:25:35 +0000
From: Rovai Antonin <Antonin.Rovai@erasme.ulb.ac.be>
Subject: [Freesurfer] color and sign of sig.mgh data
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <d0d43a1ca96fc537249ab37ed9085d25f5322aa9.camel@erasme.ulb.ac.be>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution

Hello,

I am creating sig.mgh overlays in a group analysis. On this map, I can
see some blue and red vertices, corresponding to negative and positive
values (respectively) on the map.

On the other hand, I read in the documentation that sig.mgh is a map
created by computing -log(p) (base 10, whatever).

That cannot be true, since 0<p<1, hence -log(p)>0.

After some exploration I came up with the following guess: sig.mgh is
actually -sign(z)*log(p). (That is of course very useful to quickly
interpret the maps.)

Question 1: is this guess correct?
Question 2: where is the piece of documentation I missed where this is
explained? (I am asking this because I feel like I am missing a lot on
the details on the machinery behind FS commands...)

Cheers
Antonin

H?pital Erasme - ULB
Cliniques universitaires de Bruxelles
Route de Lennik 808 - B - 1070 Bruxelles
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------------------------------

Message: 7
Date: Tue, 10 Nov 2020 07:17:49 -0800
From: Maurizio Bergamino <maurizio.bergamino@gmail.com>
Subject: [Freesurfer] Postdoctoral Fellowship in advanced
        multi-parametric imaging in Parkinson?s disease, Alzheimer?s disease,
        and healthy aging
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <CAPoSmHEA2H4joX-WXVCN19_d202i57oTindrhLzTX+Fm05CUuA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution

My Lab, at Barrow Neurological Institute (Phoenix, AZ), is looking for a
Postdoc.
For more information email to:
Ashley M. Stokes, Ph.D.
Assistant Professor // Division of Neuro-Imaging Research Barrow
Neurological Institute
*Ashley.Stokes@BarrowNeuro.org*
and/or
Ryan R. Walsh, M.D., Ph.D., FAAN
Associate Professor // Muhammad Ali Parkinson Center Department of
Neurology // Barrow Neurological Institute
*Ryan.Walsh@BarrowNeuro.org*

A postdoctoral fellowship position (fully funded for up to three years) is
available at Barrow Neurological Institute (BNI) working with Ashley
Stokes, PhD, and Ryan R. Walsh, MD, PhD, as part of a rapidly growing
collaborative research effort between the Division of Neuro-Imaging
Research, Department of Neurology, and Muhammad Ali Parkinson Center. The
position will primarily focus on the development, application, and analysis
of advanced MRI methods in the context of both Parkinson?s disease and
Alzheimer?s disease, as well as dementia with Lewy bodies and healthy
cognitive aging, expanding upon recent novel approaches developed by this
multi-modal lab. These methods include advanced functional, diffusion,
perfusion, and structural imaging methods, with an emphasis on novel
mathematical/signal processing approaches to provide a more comprehensive
understanding of neurodegenerative diseases and normal brain aging across
structural, functional, and perfusion signatures, including their mutual
interdependence.

BNI is the world?s largest dedicated neurological disease treatment and
research institution, and the Muhammad Ali Parkinson Center at BNI is a
recognized leader in the field. Outstanding institutional resources,
including 1.5T and 3T Philips clinical MRI, a research-dedicated Philips 3T
MRI, a 7T preclinical Bruker MRI, microCT, microPET, and optical imaging
scanners are available at BNI. The Division of Neuro-Imaging Research has a
strong history of imaging excellence and is currently expanding. BNI is a
major hub for neuroscience research, including both basic and translational
neuroscience, with a wide range of internationally-recognized neurology
subspecialties. Barrow Neurological Foundation provides robust
philanthropic support exceeding $18M per annum, 100% of which benefits
patient care, research and education at BNI.

Applicants should have a PhD in physics, engineering, mathematics, computer
science, or a related discipline. Competitive candidates will have
expertise in signal processing and/or functional MRI and be interested in
developing novel approaches to analysis of MRI-based signals. This position
is available immediately and offers competitive compensation and benefits.

Phoenix is the 5th largest metropolitan in the United States and the 2nd
fastest growing city. Phoenix is a beautiful place to live and work,
boasting more days of sunshine and a lower cost of living than most
comparable cities. A rich culture, including theatre, concerts, museums,
sports, and great food, are easily found in Phoenix. With a moderate
climate most of the year, many Phoenicians enjoy an active lifestyle of
hiking, cycling, rock climbing, swimming, and golf.

Interested applicants should send a current CV, including the names of
three references, to both:

*Ashley M. Stokes, Ph.D.Assistant Professor // Division of Neuro-Imaging
Research Barrow Neurological Institute Ashley.Stokes@BarrowNeuro.org*

*Ryan R. Walsh, M.D., Ph.D., FAANAssociate Professor // Muhammad Ali
Parkinson Center Department of Neurology // Barrow Neurological Institute
Ryan.Walsh@BarrowNeuro.org*
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------------------------------

Message: 8
Date: Tue, 10 Nov 2020 13:43:37 +0000
From: "Snedden, Ali" <Ali.Snedden@nationwidechildrens.org>
Subject: Re: [Freesurfer] Freesurfer 7.1.0 on CentOS 8.1 {Disarmed}
To: fsbuild <fsbuild@contbay.com>, "freesurfer@nmr.mgh.harvard.edu"
        <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <D2184349-F467-4371-BD74-18B3B4FE0705@nationwidechildrens.org>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution

Hello,

Thank you for the reply.

1.  Regarding the Nvidia drivers, we don?t have GPUs in most of our nodes (which is where I?m running freeview from).  The CPUs should be doing all the rendering in this case.
2.  I am the administrator of this cluster, so that isn?t an issue on my end.
3.  I pulled one of our CentOS 8.1.1911 nodes out of the cluster and installed freesurfer-CentOS8-7.1.0-1.x86_64.rpm locally using rpm.
4.  When I run /usr/local/freesurfer/7.1.0-1/bin/freeview, I get :

r1pl-hpcf-n09: ~$ /usr/local/freesurfer/7.1.0-1/bin/freeview

QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-aps003'

MESA-LOADER: failed to open swrast (search paths /usr/lib64/dri)

libGL error: failed to load driver: swrast

Aborted (core dumped)

And the /var/spool/abrt/ccpp-2020-11-10-08\:26\:55-23032/core_backtrace is attached.  If you can?t view it, I can paste it into an email.  It looks very similar to the original backtrace that I pasted before.  Even with the rpm installed as intended (i.e. in /usr/), it seems that not be functioning correctly.   It still seems to me that it is failing in the vtkXOpenGLRenderWindow::CreateAWindow() function.  The top of the trace is glibc, but everything calls glibc in the end.  It isn?t clear if this is a glibc, vtk or some other issue.

Thoughts?

Best regards,

Ali

From: fsbuild <fsbuild@contbay.com>
Date: Monday, November 9, 2020 at 6:53 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Cc: "Snedden, Ali" <Ali.Snedden@nationwidechildrens.org>
Subject: Re: [Freesurfer] Freesurfer 7.1.0 on CentOS 8.1 {Disarmed}

Hello Ali,

The swrast error can happen if Nvidia grpahics drivers were installed using Nvidia?s own packages/download and then subsequently, your CentOS8 kernel was updated via the CentOS package management tools, i.e. the Nvidia software may then be incompatible with the upgraded system.  I think there are Nvidia packages in the CentOS package repos, and using those to re-install the Nvidia software could fix those kinds of errors.

Currently the freesurfer RPM install path is not relocatable.  I?m not sure relocation would help as I think admin/root privileges would still be needed to for the installation process to download and install any system system dependent packages the freesurfer RPM indicates are needed.

I would ask your IT folks (with root/admin privileges) to look into updating the Nvidia software and also install the freesurfer RPM for you.  They may already have a way to share/mount/mirror what the freesurfer RPM will install under the unique path /usr/local/freesurfer/7.1.1 from one machine to another.

-R.

On Nov 6, 2020, at 09:29, Snedden, Ali <Ali.Snedden@nationwidechildrens.org> wrote:

        External Email - Use Caution

Hello,

Thank you for the response.  I am working on a computer cluster where we install all user software on a shared filesystem.  Looking at the RPM, it does not seem that I can install it in a path of my choosing (i.e. not in /usr).

i.e..
$ rpm -qpi freesurfer-CentOS8-7.1.0-1.x86_64.rpm | head -15 | grep Relocations
Relocations : (not relocatable)

Is there a strategy for installing the rpm in a custom path?

Best,
Ali

From: fsbuild <fsbuild@contbay.com<mailto:fsbuild@contbay.com>>
Date: Thursday, November 5, 2020 at 11:47 PM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: "Snedden, Ali" <Ali.Snedden@nationwidechildrens.org<mailto:Ali.Snedden@nationwidechildrens.org>>
Subject: Re: [Freesurfer] Freesurfer 7.1.0 on CentOS 8.1

Hello Ali,

I would try using the RPM installer which should at least check some dependencies on X packages, system libraries, etc.,

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- R.

On Nov 5, 2020, at 22:39, Snedden, Ali <Ali.Snedden@nationwidechildrens.org> wrote:

        External Email - Use Caution

Hello,

I?ve seen a couple mentions on the list-serv about difficulties using Freesurfer on CentOS 8.   My issue is likely similar, but I have a few more details.  I downloaded freesurfer-linux-centos8_x86_64-7.1.0.tar.gz.   When I launch `freeview`, it pops up a white/empty X window for a moment and then quickly disappears.

E.g.
$ freeview
MESA-LOADER: failed to open swrast (search paths /usr/lib64/dri)
libGL error: failed to load driver: swrast
Aborted (core dumped)

I vaguely recall that the libGL errors _aren?t_ fatal.  I?ve seen them with other X applications.  Digging around the abort logs, I found the stack trace (see end of email).

Do you have thoughts on this?  I thought it might be a VTK compatibility issue, but that is a guess at best.

Best regards,
Ali

###################### The stack trace ########################

[ccpp-2020-11-05-09:15:34-22241]# cat core_backtrace
{   "signal": 6
,   "executable": "/gpfs0/export/apps/opt/freesurfer/7.1.0/bin/freeview"
,   "only_crash_thread": true
,   "stacktrace":
      [ {   "crash_thread": true
        ,   "frames":
              [ {   "address": 140352624871839
                ,   "build_id": "f796584f6ea7bb2e49cfd09412b9c6ec86eaf0fc"
                ,   "build_id_offset": 227743
                ,   "function_name": "raise"
                ,   "file_name": "/usr/lib64/libc-2.28.so"
                }
              , {   "address": 140352624782581
                ,   "build_id": "f796584f6ea7bb2e49cfd09412b9c6ec86eaf0fc"
                ,   "build_id_offset": 138485
                ,   "function_name": "abort"
                ,   "file_name": "/usr/lib64/libc-2.28.so"
                }
              , {   "address": 140352824105729
                ,   "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4"
                ,   "build_id_offset": 1358593
                ,   "function_name": "vtkXOpenGLRenderWindow::CreateAWindow()"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"
                }
              , {   "address": 140352824102018
                ,   "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4"
                ,   "build_id_offset": 1354882
                ,   "function_name": "vtkXOpenGLRenderWindow::WindowInitialize()"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1..0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"
                }
              , {   "address": 140352824096013
                ,   "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4"
                ,   "build_id_offset": 1348877
                ,   "function_name": "vtkXOpenGLRenderWindow::Start()"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"
                }
              , {   "address": 140352717995302
                ,   "build_id": "c141e58a0e1cf92c2cbd3af5f59b2991aad943c6"
                ,   "build_id_offset": 1154342
                ,   "function_name": "vtkRenderWindow::DoStereoRender()"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1"
                }
              , {   "address": 140352717996715
                ,   "build_id": "c141e58a0e1cf92c2cbd3af5f59b2991aad943c6"
                ,   "build_id_offset": 1155755
                ,   "function_name": "vtkRenderWindow::DoFDRender()"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1"
                }
              , {   "address": 140352718000997
                ,   "build_id": "c141e58a0e1cf92c2cbd3af5f59b2991aad943c6"
                ,   "build_id_offset": 1160037
                ,   "function_name": "vtkRenderWindow::DoAARender()"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7.1.so.1"
                }
              , {   "address": 140352717997021
                ,   "build_id": "c141e58a0e1cf92c2cbd3af5f59b2991aad943c6"
                ,   "build_id_offset": 1156061
                ,   "function_name": "vtkRenderWindow::Render()"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingCore-7..1.so.1"
                }
              , {   "address": 140352824097713
                ,   "build_id": "32cfd4cdfa276fffd5973c44ddb4da4f74f234e4"
                ,   "build_id_offset": 1350577
                ,   "function_name": "vtkXOpenGLRenderWindow::Render()"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/vtk/libvtkRenderingOpenGL-7.1.so.1"
                }
              , {   "address": 5878611
                ,   "build_id": "0de18d9e888c309c18e5e9450078f0fa6f19efa3"
                ,   "build_id_offset": 1684307
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/bin/freeview"
                }
              , {   "address": 140352637235160
                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"
                ,   "build_id_offset": 2695128
                ,   "function_name": "QMetaObject::activate(QObject*, int, int, void**)"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"
                }
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                ,   "function_name": "QTimer::timeout(QTimer::QPrivateSignal)"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"
                }
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                ,   "function_name": "QTimer::timerEvent(QTimerEvent*)"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"
                }
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                ,   "build_id_offset": 2701227
                ,   "function_name": "QObject::event(QEvent*)"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"
                }
              , {   "address": 140352873383932
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                ,   "build_id_offset": 1447932
                ,   "function_name": "QApplicationPrivate::notify_helper(QObject*, QEvent*)"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Widgets.so.5"
                }
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                ,   "function_name": "QApplication::notify(QObject*, QEvent*)"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Widgets.so.5"
                }
              , {   "address": 140352637064112
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                ,   "build_id_offset": 2524080
                ,   "function_name": "QCoreApplication::notifyInternal2(QObject*, QEvent*)"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"
                }
              , {   "address": 140352637396158
                ,   "build_id": "e09fcae905f4b0eb9e9172fc60003dedd101a2f9"
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                ,   "function_name": "QTimerInfoList::activateTimers()"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"
                }
              , {   "address": 140352637398113
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                ,   "build_id_offset": 2858081
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1..0/lib/qt/lib/libQt5Core.so.5"
                }
              , {   "address": 140352610068093
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              , {   "address": 140352610069216
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                ,   "function_name": "QEventDispatcherGlib::processEvents(QFlags<QEventLoop::ProcessEventsFlag>)"
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/lib/qt/lib/libQt5Core.so.5"
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                ,   "build_id_offset": 421579
                ,   "file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/bin/freeview"
                } ]
        } ]
}

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Message: 9
Date: Tue, 10 Nov 2020 13:50:56 +0000
From: Michele Valotti <michele.valotti@gmail.com>
Subject: Re: [Freesurfer] trac-all -bedp error after successful -prep
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CALRy9m1vUcfRwKa9sT51V2FnGXn646cWtNnqgPpZWLqKOsRr4A@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution

solved it, turns out symlinks don't like relative paths (which I was using
in the config file for tracula), changing those to absolute paths tracula
finished with no errors

On Fri, 6 Nov 2020 at 11:38, Michele Valotti <michele.valotti@gmail.com>
wrote: