Freesurfer September 2019

freesurfer@nmr.mgh.harvard.edu

93 participants
143 discussions

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*

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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

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Freesurfer September 2019