Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30063 discussions

QC on CVS registration
by Mehta, Chintan 22 Nov '17

22 Nov '17

Dear FreeSurfer users, I'm using FS 6.0. I registered MRI scans to the CVS-Avg35 template (mri_cvs_register) and viewed output. While the nonlinear warp of the scan to the template looked completely fine, the warping of the automatic segmentation (aseg) did not look as "clean". Attached is a snapshot of the subject's "aseg" warped to the cvs template: "ASEG_final_CVSmorphend_tocvs-avg35.png". Also attached is a snapshot at the same slice of the ASEG of the CVS template (shipped with FS): "ASEG_template-cvs-avg35.png". This subject's "aseg" warped to CVS is typical of others in my sample. The aseg look completely fine in their respective anat spaces. The aseg warped to CVS looks splotchy. Is the splotchiness in a subject's ASEG warped to CVS template inevitable due to how registration works? With smoothing, I imagine it would look much nicer and would be almost entire in line with the ASEG of the template. As such, is it recommended that one smooth spatial maps registered to CVS template when running GLM over measures like Apparent Diffusion Coefficient (ADC) or Fractional Anisotropy (FA)? Thank you. Best, Chintan

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Re: [Freesurfer] Skullstrip commands not working {Disarmed}
by Arsenije Subotic 22 Nov '17

22 Nov '17

Hi Bruce, I performed the -autorecon-pial as a means of regenerating the surfaces as instructed on the Freesurfer skull strip tutorial. The brainmask.mgz file does not have the skull but it has some dura left over. The issue I had before was that the skull would re-appear after the subject finished processing and the surfaces would be outlined on the dura and skull. Would it be okay if I could send screenshots of the my processed subject? Thanks for your help. Arsenije ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Wednesday, November 22, 2017 11:09 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 165, Issue 35 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Job opening: postdoc in AFNI group of NIH (P Taylor) 2. Re: Problems when loading surface and mesh showing vertices (Rosalia Dacosta Aguayo) ---------------------------------------------------------------------- Message: 1 Date: Wed, 22 Nov 2017 12:50:37 -0500 From: P Taylor <neon.taylor(a)gmail.com> Subject: [Freesurfer] Job opening: postdoc in AFNI group of NIH To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAB790KVuR-gAU__TTz0CoGSTFriKNEPCrDSSxg9wAdK3qBF+GQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello- The Scientific and Statistical Computing Core (a.k.a. the AFNI group) at the NIMH, NIH (Bethesda, MD, USA) is lookin' to hire a postdoc, particularly someone with C and/or C++ experience, with Python and OpenGL skills also being quite useful. If you like problem solving and working with a fun group of people, then check out the attached advertisement for details. (And please feel free to forward on.) --pt

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Job opening: postdoc in AFNI group of NIH
by P Taylor 22 Nov '17

22 Nov '17

Hello- The Scientific and Statistical Computing Core (a.k.a. the AFNI group) at the NIMH, NIH (Bethesda, MD, USA) is lookin' to hire a postdoc, particularly someone with C and/or C++ experience, with Python and OpenGL skills also being quite useful. If you like problem solving and working with a fun group of people, then check out the attached advertisement for details. (And please feel free to forward on.) --pt

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Problems with FtpFileExchange
by Rosalia Dacosta Aguayo 22 Nov '17

22 Nov '17

Dear FreeSurfer Developers, I am having problems with FtpFileExchange. I am trying to upload a compressed file Bruce asked me to upload and it seems I am missing something in the last point of the instructions: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange *What I have done till now*: rosalia@rosalia-Lenovo-Y520-15IKBN:~$ ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu. 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit consent to our Acceptable Use Policy outlined at 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php 220- 220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either 220- 220-229 Entering Extended Passive Mode 220- 220- and nothing happens OR 220- 220-229 Entering Extended Passive Mode 220-500 Bad EPRT protocol. 220- 220- try issuing the EPSV command prior to GET or PUT. 220- 220 Name (surfer.nmr.mgh.harvard.edu:rosalia): anonymous 331 Please specify the password. Password: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp> cd transfer/incoming 250 Directory successfully changed. *What I do not understand* *ftp> put filename.txt* >From this *red* point I have no idea about how to include my compressed file S_001.zip. On the other hand, he asked me to rar and compress the file...I am sorry but I am stuck here and I have no idea how to fix this. Any help would be much appreciate. I have proved with Krusader and with FileZilla and it does not work either... Thank you for your time, Kind regards, Rosalia

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Tessellation: factors that could affect number and size of faces
by Avideh Gharehgazlou 22 Nov '17

22 Nov '17

Dear FreeSurfer experts, I have a question regarding the tessellation step, in which the surface is covered by a mesh of triangles. 1. How would the number/sizes of triangles be affected/ alter as a result of different brain volumes/sizes of different subjects? i.e. would a subject with a bigger brain volume have greater number of triangles compared to a subject with a smaller brain volume? Or will the subject have the same number of triangles, but larger triangles instead? 2. I am aware that the triangles are not uniform like the voxels in a VBM... within a particular subject, how are the sizes of triangles determined in different parts of the brain? What determines which parts of the brain will have smaller/larger triangles compared to other parts of the brain? Would really appreciate your input, Thanks, Avi CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. AVIS DE CONFIDENTIALITÉ : Ce message électronique, ainsi que tout fichier qui y est joint, est reserve à l'usage exclusif du destinataire visé et peut contenir des renseignements confidentiels et privilégiés. Toute lecture, utilisation, divulgation ou distribution non autorisée est interdite. Si vous n'êtes pas le destinataire visé, veuillez en aviser l'expéditeur par retour de courriel et détruire toutes les copies du message original.

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Skullstrip commands not working
by Arsenije Subotic 21 Nov '17

21 Nov '17

Dear experts, I recently finished processing a subject for whom I had performed a skullstrip on the brainmask volume. I decreased the watershed parameter and re-examined the brainmask and the portion of the skull was gone, although some dura was left over. I did a recon-all using the following command: recon-all -autorecon-pial -subjid <subject name> However, when recon was finished, I noticed that the skull re-appeared and the surfaces were outlined on it. I went back and tried g-cut to remove the little dura that was left over, but that also did not work. I tried varying the watershed parameters again but I keep getting the same result. Is there any other underlying issue that may be at fault? Thanks for your help, Arsenije

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Re: [Freesurfer] T1 and brainmask wonky: Pieces of putamen missing
by diana hobbs 21 Nov '17

21 Nov '17

Update to my first email: Hello again FS Developers and anyone experiencing the same problems, A colleague of mine has found what we think has already been addressed in the following link: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-November/048666… >From the sounds of it, this doesn't seem to be a real issue; however, I would love to better understand why this doesn't matter in the long run, i.e. why the brainmask does not later affect parcellation of subcortical regions(?). Thank you for your time! Diana

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hippocampal subfields stats
by Donatas Sederevicius 21 Nov '17

21 Nov '17

Dear Freesurfer Developers, I’ve run the new longitudinal hippocampal subfields segmentation using Freesurfer’s developer version. Then I decided to extract stats for each hierarchy: HBT, FS60 and CA. I used the following command, for example: mri_segstats —seg lh.hippoAmygLabels-T1.long.v20.CA.mgz —ctab-default —sum output.txt I got what I wanted but decided to compare the results of one subject for Hippocampal_tail for each hierarchy and with the text file lh.hippoSfVolumes-T1.long.v20.txt. I got the following volume values: lh.hippoSfVolumes-T1.long.v20.txt: 583.65 HBT: 593.4 FS60: 593.4 CA: 598.3 I wonder how do you actually extract stats that are present in lh.hippoSfVolumes-T1.long.v20.txt file? What is the reason for different values? I’m very curious since I cannot get the exact same stats as in the lh.hippoSfVolumes-T1.long.v20.txt file. Thanks a lot! Donatas

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Re: [Freesurfer] Problems when loading surface and mesh showing vertices
by Rosalia Dacosta Aguayo 21 Nov '17

21 Nov '17

Dear Bruce, I am using FileDropv2.0... I hope you and all the members of the list can access into this subject. Thank you for your help in advance, Rosalia 2017-11-21 18:35 GMT+01:00 Rosalia Dacosta Aguayo <rdacostaa(a)gmail.com>: > Sorry Bruce, > > Here is the problem I wanted to avoid: > > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer > FSFAST_HOME /usr/local/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/local/freesurfer/subjects > MNI_DIR /usr/local/freesurfer/mni > FSL_DIR /usr/share/fsl/5.0 > bash: /opt/minc/minc-toolkit-config.sh: No such file or directory > rosalia@rosalia-Lenovo-Y520-15IKBN:~$ $ ftp surfer.nmr.mgh.harvard.edu > $: command not found > rosalia@rosalia-Lenovo-Y520-15IKBN:~$ ftp surfer.nmr.mgh.harvard.edu > Connected to surfer.nmr.mgh.harvard.edu. > 220-This is the Martinos Center Anonymous FTP service. Use of this > site > 220-shows implicit consent to our Acceptable Use Policy outlined > at > 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php > > 220- > 220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either > 220- > 220-229 Entering Extended Passive Mode > 220- > 220- and nothing happens OR > 220- > 220-229 Entering Extended Passive Mode > 220-500 Bad EPRT protocol. > 220- > 220- try issuing the EPSV command prior to GET or PUT. > 220- > 220 > Name (surfer.nmr.mgh.harvard.edu:rosalia): anonymous > 331 Please specify the password. > Password: > 530 Login incorrect. > Login failed. > ftp> > > > > 2017-11-21 18:31 GMT+01:00 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > >> sorry, I don't understand. I haven't gotten anything, and it is likely >> way too big to email. If you upload it to the FTP site no one from the >> outside will have access to it >> >> cheers >> Brue >> >> On Tue, 21 Nov 2017, Rosalia Dacosta Aguayo wrote: >> >> Sorry Bruce, >>> >>> I have sent it to your email directly...in order to avoid the process of >>> uploading the data...because I am not familiar with it. >>> >>> Kind regards, >>> Rosalia >>> >>> 2017-11-21 18:25 GMT+01:00 Rosalia Dacosta Aguayo <rdacostaa(a)gmail.com>: >>> Sorry Bruce, >>> >>> I prefer sending it to your email directly, then if you want to make >>> it available to the other memebrs, there is not problem at all... >>> >>> Kind regards, >>> Rosalia >>> >>> 2017-11-21 18:17 GMT+01:00 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >>> tar and gzip the entire subject dir and upload it >>> following these instructions: >>> >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange >>> >>> On Tue, 21 Nov 2017, Rosalia Dacosta Aguayo wrote: >>> >>> Hi Bruce, >>> >>> Thank you for answering. >>> >>> Not, it is not a bug...in fact >>> recon-all...-all had not problems. Just I was >>> looking at the outputs...and as I am running >>> FreeSurfer for my first time I >>> wanted to ask about if this was a problem or I >>> can go on.... >>> >>> Where I should upload the subject and which >>> files? I mean, in order to do >>> not overload the mail list... >>> >>> Kind regards, >>> Rosalia >>> >>> 2017-11-21 18:09 GMT+01:00 Bruce Fischl >>> <fischl(a)nmr.mgh.harvard.edu>: >>> hmmm, that is odd looking. Can you >>> upload that subject so we can >>> see if >>> it is just a display bug or not? >>> On Tue, 21 Nov 2017, Rosalia Dacosta >>> Aguayo >>> wrote: >>> >>> > Dear FreeSurfer Developers, >>> > >>> > I am checking the OutputData_freeview >>> after running recon-all >>> following your >>> > tutorial: >>> > >>> >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputD >>> ata_freeview >>> > >>> > I have loaded T1.mgz, wm.mgz, >>> brainmask.mgz and aseg.mgz, and >>> then the >>> > surfaces: rh.pial, rh.white, lh.pial >>> and lh.white. >>> > >>> > In general, I did not see any >>> problem...but when I wanted to >>> see the >>> > surface&mesh with vertices I saw >>> something estrange I do not >>> know if it is a >>> > problem or it is normal (see the >>> vertices in the temporal pole >>> in grey >>> > scale)...as this is my first run with >>> FreeSurfer. I attach you >>> the image. >>> > >>> > 1. FreeSurfer version: >>> > >>> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c >>> > 2. Platform: CentOS release 6.7 >>> > 3. uname -a: Linux >>> rosalia-PORTEGE-Z930 4.4.0-98-generic >>> #121-Ubuntu SMP Tue >>> > Oct 10 14:24:03 UTC 2017 x86_64 x86_64 >>> x86_64 GNU/Linux >>> > 4. Recon-all.log; see attached >>> (although it ended without >>> errors) >>> > >>> > I haven't come across this error in my >>> searches, but I may be >>> using the >>> > wrong key terms. Would anyone be able >>> to point me in the right >>> direction or >>> > trouble-shoot fixing this? >>> > >>> > Thank you for your time, >>> > Rosalia >>> > >>> > >>> > >>> > >>> > >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended >>> only for the person to whom >>> it is >>> addressed. If you believe this e-mail was sent >>> to you in error and the >>> e-mail >>> contains patient information, please contact >>> the Partners Compliance >>> HelpLine at >>> 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 >>> dispose of the e-mail. >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person >>> to whom it is >>> addressed. If you believe this e-mail was sent to you in error >>> and the e-mail >>> contains patient information, please contact the Partners >>> Compliance HelpLine at >>> 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 >>> dispose of the e-mail. >>> >>> >>> >>> >>> >

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Problems when loading surface and mesh showing vertices
by Rosalia Dacosta Aguayo 21 Nov '17

21 Nov '17

Dear FreeSurfer Developers, I am checking the OutputData_freeview after running recon-all following your tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview I have loaded T1.mgz, wm.mgz, brainmask.mgz and aseg.mgz, and then the surfaces: rh.pial, rh.white, lh.pial and lh.white. In general, I did not see any problem...but when I wanted to see the surface&mesh with vertices I saw something estrange I do not know if it is a problem or it is normal (see the vertices in the temporal pole in grey scale)...as this is my first run with FreeSurfer. I attach you the image. 1. FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2. Platform: CentOS release 6.7 3. uname -a: Linux rosalia-PORTEGE-Z930 4.4.0-98-generic #121-Ubuntu SMP Tue Oct 10 14:24:03 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux 4. Recon-all.log; see attached (although it ended without errors) I haven't come across this error in my searches, but I may be using the wrong key terms. Would anyone be able to point me in the right direction or trouble-shoot fixing this? Thank you for your time, Rosalia

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