Re: [Freesurfer] PALM Analysis
Hi Doug I wanted to follow up this email and ask you a question. I see in the fspalm page, it says "You can use fspalm with both volume- and surface-based analyses; it will figure everything out". Considering your reply to the below email, I'm wondering if we can use fspalm for subcortical analysis or not? I appreciate very much any comments on it. Thanks Mona From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: Monday, September 2, 2019 10:32 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PALM Analysis 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] PALM Analysis
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=3640=36498=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=3640=36498=https://www.ohbmtrainees.com/mentoring-programme/> >> and check our previous publication >> <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2=3640=36498=https://onlinelibrary.wiley.com/doi/full/10./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=3640=36498=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 + >> From: "Harikumar, Amritha" >> Subject: [Freesurfer] PALM Analysis >> To: "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 + >> From: "Greve, Douglas N.,Ph.D." >> Subject: Re: [Freesurfer] PALM Analysis >> To: "freesurfer@nmr.mgh.harvard.edu" >> Message-ID: >> 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 >&
[Freesurfer] PALM Analysis
ight 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=3640=36498=https://www.ohbmtrainees.com/mentoring-programme/> > and check our previous publication > <https://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2=3640=36498=https://onlinelibrary.wiley.com/doi/full/10./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=3640=36498=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 + > From: "Harikumar, Amritha" > Subject: [Freesurfer] PALM Analysis > To: "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 + > From: "Greve, Douglas N.,Ph.D." > Subject: Re: [Freesurfer] PALM Analysis > To: "freesurfer@nmr.mgh.harvard.edu" > Message-ID: > 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, M
Re: [Freesurfer] PALM Analysis
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] PALM Analysis
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
