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(Revised) Clusterwise correction for multiple comparisons
by Gwang-Won Kim 03 Sep '19

03 Sep '19

1 0

mri_surf2surf without sphere.reg
by Caspar M. Schwiedrzik 03 Sep '19

03 Sep '19

External Email - Use Caution Hi! I am having some issues projecting retinotopic mapping data from a monkey analyzed in surface space onto its surface using rtview. The issue seems to be that the data need to be converted into paint format through mri_surf2surf, and that we do not have a ?h.sphere.reg file because the surface is not aligned to a template. Is it possible to run mri_surf2surf without reference to ?h.sphere.reg somehow? I tried with --s instead of source and target subject, but that didn't work. Alternatively, can we provide an identity matrix for ?h.sphere.reg, perhaps through mris_register? Any advice would be appreciated. Thanks, Caspar

2 2

qdec contrast and data extraction
by Maximo, Jose Omar 03 Sep '19

03 Sep '19

External Email - Use Caution Hi, I have a question: My design is 2 groups (HC and Patients in that respective order) and 2 nuisance factors (age and eTIV). When I look at the average volume difference between the 2 groups, I get blue and red clusters. I presume the color coding is where each group is greater than the other (Blue = Patients > HC and Red = HC > Patients). Then, I processed to extract individual values from each cluster in order to plot them. When I extract data from the blue clusters and plot them, the two groups show no difference in thickness at all, whereas when I look at volume, HC show more than patients in blue clusters (see attached figure). I would assume that both figures would show patients > HC based on the negative statistic. Am I interpreting the colors wrong? Or am I doing something wrong? These are my steps 1) After applying montecarlo correction, I drew my ROIs to extract the data from; 2) map it onto every single subject; and then 3) used mris_anatomical_stats to extract the data from each subject. Any suggestions are welcome. Best, Omar Jose O. Maximo, Ph.D. | Postdoctoral Fellow Department of Psychiatry & Behavioral Neurobiology UAB School of Medicine University of Alabama at Birmingham Cell Phone: (619) 252-3492 Email: jomaximo(a)uabmc.edu<mailto:jomaximo@uabmc.edu>

2 1

Reconall with no-MPRAGE T1w image?
by Rovai Antonin 03 Sep '19

03 Sep '19

External Email - Use Caution Hello, From the ReconAllTable (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) I see that the mri_normalize step (producing the T1.mgz file) has the -mprage option. I have two questions: 1. What is this option doing exactly? There is no description in the mri_normalize man page (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_normalize) similarly, the CLI help doesn’t mention this option. 2. How do I change this when launching a ReconAll without re-writing a custom pipeline? (For context our T1 is not MPRAGE and we had some segmentation issues so this is an attempt to debug this). Thanks for you help AR [Hôpital Erasme] Lien vers Disclaimer<http://www.erasme.ulb.ac.be/email-disclaimer>

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Question about how to build .gca files from non-human atlas and images
by arsene ella 03 Sep '19

03 Sep '19

External Email - Use Caution *Dear **Freesurfer experts,* *I’ve built an atlas of structures of a non-human average brain and now **I would like to build **its** .gca files from scratch. **From the Freesurfer mailing list, I saw that this is possible using **rebuild_gca_atlas.csh* *which trains labelled brai**ns (**seg_edited.mgz**) and their intensity volumes (it is said to use the **norm.mgz** for this purpose) from several subjects through **mri_ca_train**. **My questions are :**1) How to normalize my native intensity volume to a **norm.mgz** volume without .gca and .lta files asking by **mri_ca_normalize **?**Y**ou’ve suggested to give **mri_ca_normalize** a flag to tell it to use a manual segmentation instead of the gca by trying **-seg <manual seg volume>**. Then the gca name won't matter - it should ignore it… I tried this as followed :**let : **- **Brain_Template_T1_MPR.mgz ** be my intensity native volume**- **Brain_Cortex_Atlas.mgz* * be my manual segmented volume**- **Brain_Template_T1_MPR_norm.mgz* * be **my **norm** output** volume* *Command lines :**mri_ca_normalize** Brain_Template_T1_MPR.mgz **-seg** Brain_Cortex_Atlas.mgz Brain_Template_T1_MPR_norm.mgz**gave the following error message :**reading 1 input volume**reading atlas from '-seg'...**GCAread(-seg): could not open file**No such file or directory**mri_ca_normalize: could not open GCA -seg.**No such file or directory* *mri_ca_normalize* *-seg ** Brain_Cortex_Atlas.mgz Brain_Template_T1_MPR.mgz Brain_Template_T1_MPR_norm.mgz**gave the following message and stopped:**using segmentation volume /home/arsene/Bureau/FS_GCA/FS_SHEEP_CGA/Brain_Cortex_Atlas.mgz to generate control points...**usage: mri_ca_normalize [<options>] <inbrain1> <inbrain2> ... <atlas> <transform file> <output1> <output2> ...* *What is wrong with theses **mri_ca_normalize* *commands ?* *2) My second question is to know how to transfert labels from my* *manual seg**mented** volume **(ex : **atlas.mgz**) to each single image volume (ex : vol1**.mgz**) ?**You’ve suggested to use **mri_label2label**, but **I didn’t see anything allowing me to do a **volume_to_volume** transfert **from **its **–help**…** If I got it wrong, could you suggest a command ?* *cheers* *Arsene*

1 0

OHBM International Mentoring Programme Sign-up {Disarmed}
by Meena M. Makary 02 Sep '19

02 Sep '19

External Email - Use Caution Hi all, Between September 1st and September 31st 2019, registration for the fourth round of the Online International Mentoring Programme organized and coordinated by the OHBM Student and Postdoc Special Interest Group <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…> will take place. In the programme, every OHBM member can become an (online) mentor or a mentee to another OHBM member(s) for a period of approximately one year (October-June). During this time, the mentor can support the mentee to grow in academia by providing advice on topics such as—but not limited to—personal development, grant writing, and work-life balance. In response to the feedback from previous participants and the increased interest of mentees in industry, we have also invited a number of mentors from industry to join us for this new round. If you are interested in being a mentor and/or mentee, please fill out this short registration form <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…> and you will be contacted with further details. If you participated in any of the previous rounds and would like to further take part in the programme, you have two possible ways (It is possible to choose both options): 1. If you would like to continue being paired with your current mentors/mentees, please first discuss this with your mentoring partner. In this case, please do not re-subscribe for the programme and please delegate the mentee to fill in this feedback form <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…> for us. 2. If you would like to apply for new mentors/mentees, you will be able to do so using the registration link above. Please feel free to forward this message to your colleagues. Please also forward this email to former researchers working in industry, if you know any, as we are still looking for more industry representatives to join the programme as mentors this year. We would like to thank all the OHBM mentors and mentees who participated in the previous three rounds of the programme! The third round of the programme is now ending. We hope that most of you had an opportunity to meet in person during the OHBM Annual Meeting in Rome. If you have feedback for us, please contact us at ohbmtrainees(a)gmail.com <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…>. Please share any comments which might help to further improve our programme! To find out more about the programme, please visit the OHBM Student and Postdoc SIG website <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…> and check our previous publication <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…>. If you have any questions about the programme, please contact us at ohbmtrainees(a)gmail.com <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3…> . We hope to welcome you in the programme very soon! Best regards, — *Meena M. Makary, Ph.D.* Assistant Professor | Cairo University <http://bmes.cufe.edu.eg/> Postdoctoral Fellow | Radiology, Harvard Medical School <https://connects.catalyst.harvard.edu/Profiles/display/Person/176550> Postdoctoral Fellow | Athinoula A. Martinos Center, MGH <https://www.nmr.mgh.harvard.edu/user/4550386> Career Development and Mentoring Manager | OHBM Student and Postdoc SIG <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449>

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Two questions about flac_desmat.m for retinotopy analysis in fsfast
by Caspar M. Schwiedrzik 02 Sep '19

02 Sep '19

External Email - Use Caution Hi Doug, I have two quick questions about the analysis of polar angle maps: 1. Does the analysis take the HRF (lag etc.) into account? 2. Our stimulation starts at 12 for clockwise and counter clockwise. I found this older post https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-August/025241.ht… specifying changes to flac_desmat.m to account for that. I was wondering whether to change case {'fourier'} and/or case {'abret'}? This is using version 5.3. Thank you! Caspar

1 0

syntax error near unexpected token 'newline'
by michele rizzi 31 Aug '19

31 Aug '19

External Email - Use Caution Dear All during freesurfer installation, I type export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh and I have this error syntax error near unexpected token 'newline' can you help me? thanks Mike

5 7

Re: [Freesurfer] R: R: syntax error near unexpected token 'newline'
by fsbuild 31 Aug '19

31 Aug '19

External Email - Use Caution Yes, as Viviana said, you need to specify the path to the Applications folder by using a leading slash “/“ character. You can test that path /Applications/freesurfer/subjects is OK by opening the terminal application and then typing at the dollar sign prompt, $ ls /Applications/freesurfer/subjects ... which should not give you an error and show some files are there. Unless someone changed the shell preferences for your account on the Mac, then the default shell at the $ prompt in the terminal window is bash shell for Mac OS 10.14.  There should be no need to type “bash” again (and start another shell). So in the terminal window it should work for you to type the lines after the dollar sign prompt  (you could cut and paste the below), and then see if you get the same output. $ ls -d /Applications/freesurfer/Applications/freesurfer $ export FREESURFER_HOME=/Applications/freesurfer$ echo $FREESURFER_HOME/Applications/freesurfer $ ls $FREESURFER_HOME/SetUpFreeSurfer.sh/Applications/freesurfer/SetUpFreeSurfer.sh $ source $FREESURFER_HOME/SetUpFreeSurfer.sh If the “source" command results in an error, then you can try to see what failed by running the shell script with “sh -x” instead of “source”. $ sh -x $FREESURFER_HOME/SetUpFreeSurfer.sh If running the script with “sh -X” does not end with a “return 0” statement displayed on the terminal, then you cost cut and paste the last several lines before the error and email it back to us. - R. On Aug 31, 2019, at 00:04, Viviana Siless <viviana.siless(a)gmail.com> wrote:        External Email - Use Caution        Hi, I think you are just mistyping it, if the subjects dir is in "/Applications/freesurfer/subjects/ " the command  should be:export SUBJECTS_DIR=/Applications/freesurfer/subjects/ ( instead of  export SUBJECTS_DIR=<Applications/freesurfer/subjects>)Viv On Fri, Aug 30, 2019 at 4:35 PM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote:oh, the export command is failing? You mentioned you weren't running bash (which is the shell that knows what to do with an export command). Can you install bash? If not, you can use setenv instead of export and the .csh file instead of the .shOn Fri, 30 Aug 2019, michele rizzi wrote:> >         External Email - Use Caution        > > > I put > > > export SUBJECTS_DIR=<Applications/freesurfer/subjects>> > > > but again I get > > > > -bash: syntax error near unexpected token `newline'> > > > > > >_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Substancia-Nigra ROI
by Gwang-Won Kim 30 Aug '19

30 Aug '19

2 1

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