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
