mri_glmfit-sim will do it, GRF or permutation On 9/4/19 1:33 PM, Harikumar, Amritha wrote: > Hello, > > Thanks for letting me know regarding running fsPalm in your previous message. > My next question is - what command can we use in Freesurfer that can run > multiple comparison testing for subcortical regions? If not fsPalm, is there > another function that will perform this? > > Thanks, > Amritha > > > Amritha Harikumar > Clinical Research Coordinator > Holt Emotion and Social Neuroscience Lab > Department of Psychiatric Neuroimaging > Martinos Center for Biomedical Imaging > Massachusetts General Hospital > ___________________________ > 149 13th Street, Rm 2620A > Charlestown, MA 02129 > Phone: 617-724-3283 > > > >> On Sep 3, 2019, at 6:06 AM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: >> >> Send Freesurfer mailing list submissions to >> freesurfer@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-requ...@nmr.mgh.harvard.edu >> >> You can reach the person managing the list at >> freesurfer-ow...@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. OHBM International Mentoring Programme Sign-up {Disarmed} >> (Meena M. Makary) >> 2. PALM Analysis (Harikumar, Amritha) >> 3. Re: PALM Analysis (Greve, Douglas N.,Ph.D.) >> 4. Discrepancy between thresholded surface and cluster labels >> (Bronwyn Overs) >> 5. Reconall with no-MPRAGE T1w image? (Rovai Antonin) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Mon, 2 Sep 2019 12:19:45 -0400 >> From: "Meena M. Makary" <meena.maghari...@gmail.com> >> Subject: [Freesurfer] OHBM International Mentoring Programme Sign-up >> {Disarmed} >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: >> <CAF4GKtcDD7AdkJFUhQ9KTq_ypOhEo+5Z_Qn+wz6u4kFrvjv=+q...@mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> 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=3640&contactID=36498&origURL=https://www.ohbmtrainees.com/mentoring-programme/> >> 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=3640&contactID=36498&origURL=https://www.surveymonkey.com/r/WNBTZXC> >> 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=3640&contactID=36498&origURL=https://www.surveymonkey.com/r/VH95VY8> >> 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 ohbmtrain...@gmail.com >> <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3640&contactID=36498&origURL=mailto:ohbmtrain...@gmail.com>. >> 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=3640&contactID=36498&origURL=https://www.ohbmtrainees.com/mentoring-programme/> >> and check our previous publication >> <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3640&contactID=36498&origURL=https://onlinelibrary.wiley.com/doi/full/10.1111/ejn.14320>. >> If you have any questions about the programme, please contact us at >> ohbmtrain...@gmail.com >> <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=3640&contactID=36498&origURL=mailto:ohbmtrain...@gmail.com> >> . >> >> >> 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> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190902/265eab84/attachment-0001.html >> >> ------------------------------ >> >> Message: 2 >> Date: Mon, 2 Sep 2019 23:46:23 +0000 >> From: "Harikumar, Amritha" <ahariku...@mgh.harvard.edu> >> Subject: [Freesurfer] PALM Analysis >> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <0c71fa4e-bc6b-4a11-bd20-940851c5f...@mgh.harvard.edu> >> Content-Type: text/plain; charset="utf-8" >> >> Hi there, >> >> I am trying to run a Permutation Analysis of Linear Models (PALM) for >> analyzing subcortical areas in the nucleus accumbens, caudate, and putamen. >> Upon trying to run the script after reading the Freesurfer wiki, I am not >> sure what it is referring to regarding applying fsPalm in MATLAB. My >> questions are - do we a.) copy paste the existing fspalm command in Matlab >> and run it after setting the two Freesurfer paths listed in the wiki, or >> what is the correct procedure to run it? I tried running it in terminal as >> well, but didn?t have any luck. My existing Matlab script has set up the two >> Freesurfer paths, and is trying to run the fsPalm command for each >> subcortical area of the three ROIs mentioned above, but that isn?t working >> either. Any help in running fsPalm would be greatly appreciated! >> >> Thanks, >> Amritha >> >> Amritha Harikumar >> Clinical Research Coordinator >> Holt Emotion and Social Neuroscience Lab >> Department of Psychiatric Neuroimaging >> Martinos Center for Biomedical Imaging >> Massachusetts General Hospital >> ___________________________ >> 149 13th Street, Rm 2620A >> Charlestown, MA 02129 >> Phone: 617-724-3283 >> >> >> >> >> >> >> ------------------------------ >> >> Message: 3 >> Date: Tue, 3 Sep 2019 02:32:10 +0000 >> From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> >> Subject: Re: [Freesurfer] PALM Analysis >> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <e6aab003-7edb-e8cf-e771-d7060d5b2...@mgh.harvard.edu> >> Content-Type: text/plain; charset="utf-8" >> >> Sorry, fsplam is only for surfaces. >> >> On 9/2/2019 7:46 PM, Harikumar, Amritha wrote: >>> Hi there, >>> >>> I am trying to run a Permutation Analysis of Linear Models (PALM) for >>> analyzing subcortical areas in the nucleus accumbens, caudate, and putamen. >>> Upon trying to run the script after reading the Freesurfer wiki, I am not >>> sure what it is referring to regarding applying fsPalm in MATLAB. My >>> questions are - do we a.) copy paste the existing fspalm command in Matlab >>> and run it after setting the two Freesurfer paths listed in the wiki, or >>> what is the correct procedure to run it? I tried running it in terminal as >>> well, but didn?t have any luck. My existing Matlab script has set up the >>> two Freesurfer paths, and is trying to run the fsPalm command for each >>> subcortical area of the three ROIs mentioned above, but that isn?t working >>> either. Any help in running fsPalm would be greatly appreciated! >>> >>> Thanks, >>> Amritha >>> >>> Amritha Harikumar >>> Clinical Research Coordinator >>> Holt Emotion and Social Neuroscience Lab >>> Department of Psychiatric Neuroimaging >>> Martinos Center for Biomedical Imaging >>> Massachusetts General Hospital >>> ___________________________ >>> 149 13th Street, Rm 2620A >>> Charlestown, MA 02129 >>> Phone: 617-724-3283 >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> ------------------------------ >> >> Message: 4 >> Date: Tue, 3 Sep 2019 14:00:22 +1000 (AEST) >> From: Bronwyn Overs <b.ov...@neura.edu.au> >> Subject: [Freesurfer] Discrepancy between thresholded surface and >> cluster labels >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: >> <1982068687.31611543.1567483222777.javamail.zim...@neura.edu.au> >> Content-Type: text/plain; charset="utf-8" >> >> External Email - Use Caution >> >> Dear Freesurfer mailing list, >> >> I am trying to get to the bottom of a discrepancy between two surface based >> images generated from the output of an LME analysis. The surfaces in row 1 >> of the attached image were generated by loading the four FDR significant >> clusters that were >100mm^2 in the cluster summary file. The surfaces in row >> 2 of the attached image were generated by loading the significance map >> generated for the same fixed effect (saved from the LME), and thresholding >> at the FDR corrected p -value. The question I have is why are there such >> large swatches of the cortical surface in the row 2 images that are labelled >> as log10 p = 5, when they are not included in the most significant and >> largest clusters that were found in the cluster summary file? >> >> >> >> Kind regards, >> >> >> >> >> >> Bronwyn Overs >> >> >> Research Assistant >> >> >> >> Neuroscience Research Australia >> Margarete Ainsworth Building >> Barker Street Randwick Sydney NSW 2031 Australia >> M 0411 308 769 T +61 2 9399 1725 >> >> >> [ http://neura.edu.au/ | neura.edu.au? ] >> >> >> >> [ https://twitter.com/neuraustralia | Twitter ] | [ >> https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ >> http://www.neura.edu.au/help-research/subscribe | Subscribe ] >> >> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190903/8566d345/attachment-0001.html >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: neura-logo-email.png >> Type: image/png >> Size: 13292 bytes >> Desc: not available >> Url : >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190903/8566d345/attachment-0002.png >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: LME_LabelsVsSurface.png >> Type: image/png >> Size: 292366 bytes >> Desc: not available >> Url : >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190903/8566d345/attachment-0003.png >> >> ------------------------------ >> >> Message: 5 >> Date: Tue, 3 Sep 2019 10:06:48 +0000 >> From: Rovai Antonin <antonin.ro...@erasme.ulb.ac.be> >> Subject: [Freesurfer] Reconall with no-MPRAGE T1w image? >> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >> Message-ID: <0f061d5c-d461-4542-9c14-f044d4c94...@erasme.ulb.ac.be> >> Content-Type: text/plain; charset="utf-8" >> >> 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 >> >> [H?pital Erasme] >> >> Lien vers Disclaimer<http://www.erasme.ulb.ac.be/email-disclaimer> >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190903/d371125b/attachment.html >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: image93f5ba.JPG >> Type: image/jpeg >> Size: 33575 bytes >> Desc: image93f5ba.JPG >> Url : >> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190903/d371125b/attachment.jpe >> >> ------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> End of Freesurfer Digest, Vol 187, Issue 2 >> ****************************************** > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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