Freesurfer November 2017

freesurfer@nmr.mgh.harvard.edu

110 participants
198 discussions

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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fsaverage template appropriate to use with pediatric population?
by Avideh Gharehgazlou 21 Nov '17

21 Nov '17

Hi experts, I have a few questions regarding the use of fsaverage template for my research: 1. Is the fsaverage template appropriate for use with pediatric population? (My sample is 6-16 years of age) 2. What possible errors can be expected ? What could possible alignment errors be? 3. Are there any regions I should expect to have more errors in? Would really appreciate a response, 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.

2 1

cuda compile help
by Meij, Henk 21 Nov '17

21 Nov '17

cuda v8 freesurfer git download from today (v6?), gtx1080ti gpus, brief env recap: 999 cd /usr/local/freesurfer-gpu.git/ 1001 export PATH=/usr/local/cuda-8.0/bin:$PATH 1002 export LD_LIBRARY_PATH=/usr/local/cuda-8.0/lib64 1004 make clean 1008 ./setup_configure | tee -a setup_configure.log 1011 ./configure --disable-Werror --with-pkgs-dir=/usr/local/centos6-x86_64-packages --prefix=/usr/local/freesurfer-6.0.0 --with-cuda=/usr/local/cuda-8.0 | tee -a configure.log 1012 time make -j4 | tee -a make.log 1013 make install [hmeij@n78 freesurfer-gpu.git]$ grep nvcc Makefile NVCC = /usr/local/cuda-8.0/bin/nvcc Q1 what causes this and how to fix, make install fails /bin/install -c fs_spmreg.glnxa64 irepifitvol.glnx64 /usr/local/freesurfer-6.0.0/bin /bin/install: cannot stat Ã¢_spmreg.glnxa64Ã¢No such file or directory /bin/install: cannot stat Ã¢epifitvol.glnx64Ã¢No such file or directory make[2]: *** [install-data-local] Error 1 make[2]: Leaving directory `/usr/local/freesurfer-gpu.git/scripts' make[1]: *** [install-am] Error 2 make[1]: Leaving directory `/usr/local/freesurfer-gpu.git/scripts' make: *** [install-recursive] Error 1 Q2 no cuda packages, maybe related to Q1 [hmeij@n78 freesurfer-gpu.git]$ ls /usr/local/freesurfer-6.0.0/bin/*cuda* /usr/local/freesurfer-6.0.0/bin/cuda_setup Thanks for any help. -Henk

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Problems after running recon-all ...-qcache
by Rosalia Dacosta Aguayo 21 Nov '17

21 Nov '17

Dear FreeSurfer Developers, I have run recon-all....-qcache after reviewing the recon-all...-all outputs in freeview..... I have been looking into: https://surfer.nmr.mgh.harvard.edu/fswiki/mris_preproc Now it seems that I could have omitted the -qcache...and I am a bit lost with the examples showed in the link. Any one could help me regarding the concatenation and how to created the FSGD file? Taking into account I would like to run a cortical thickness analysis between three groups, how I should run the ANOVA? Finally, should I have into account General Atrophy Measures such as: global average thickness for both hemispheres, only or in combination with estimated global intracranial volume as a nuissance regressors in the design? So = ANCOVA instead of ANOVA. Does anyone have any thoughts on how to trouble-shoot those problems? Kind regards, Rosalia

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Freesurfer November 2017