Freesurfer September 2019

freesurfer@nmr.mgh.harvard.edu

93 participants
143 discussions

PALM Analysis
by Harikumar, Amritha 04 Sep '19

04 Sep '19

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-request(a)nmr.mgh.harvard.edu wrote: > > Send Freesurfer mailing list submissions to > freesurfer(a)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-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)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.magharious(a)gmail.com> > Subject: [Freesurfer] OHBM International Mentoring Programme Sign-up > {Disarmed} > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CAF4GKtcDD7AdkJFUhQ9KTq_ypOhEo+5Z_Qn+wz6u4kFrvjv=+Q(a)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=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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FreeView : Tools : Volume Filter : Close
by Yasir Hadi 04 Sep '19

04 Sep '19

External Email - Use Caution Hello FreeSurfer Developers, I just want to get the Information: which parameters are used as I apply the filter *Close* on the volume dataset using the FreeView Version 2.0 Builed Jan 18 2017 16:48:55. I've searched the list and the wiki and I didn't find a similar information. Thanks :) Regards, Ysr H

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Re: [Freesurfer] PETsurf kinetic modeling with MRTM
by Chanmi Kim 04 Sep '19

04 Sep '19

External Email - Use Caution Hi Douglas, I checked dicom headers by using ‘dicom_hinfo’ command to get the information of the acquisition time that each frame was acquired. dicom_hinfo -tag 0008,0032 *.dcm Here is the information of the acquisition times: 16:40:08 16:45:08 16:50:08 16:55:08 17:00:08 17:05:08 The number of slices is 90 in each tau PET data, so each dicom file has been acquired at one of the acquisition times. (ex: ADNI3_tau_001.dcm 16:40:08, ADNI3_tau_002.dcm 16:50:08, ADNI3_tau_003.dcm 16:40:08, ... ADNI3_tau_90.dcm 17:00:08) ADNI3 dyamic PET has made up with 6 frames, and each frames took 5 min. So, I think that I can create ‘time.dat’ as below: 164008 164508 165008 165508 170008 170508 Do I use this information? Or should I change anything for making the ‘ time.dat’? Thank you, Chan ------------------------------ Message: 3 Date: Fri, 30 Aug 2019 16:27:03 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> Subject: Re: [Freesurfer] PETsurf kinetic modeling with MRTM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <de737572-1fb1-4bc8-1564-2e80e3c1ced0(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" This is the time at which each frame was acquired. It is just a list of times in seconds in a text file. You will have to go to the person who collected the data On 8/30/2019 10:25 AM, Chanmi Kim wrote: External Email - Use Caution Hello, I'd like to perform MRTM2 approach in ADNI3 tau PET data for partial volume correction (PVC). So, I've tried to do a command line as below. mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 --no-est-fwhm --nii.gz The 'mri_glmfit' required 'time.dat' which is an information of the time activity curve (TAC), however, I don't know how to get this information. Can you please let me know how to get this information? Please share any examples of 'time.dat' If there is anyone who has experience in PetSurf PVC, Chan _______________________________________________

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Compare vertexwise correlation maps
by Matthieu VANHOUTTE 04 Sep '19

04 Sep '19

External Email - Use Caution Dear experts, I would like now to determine if there is statistically difference between vertexwise correlation maps (whether one is statistically "stronger" than the other). Would there be a way to do this with Freesurfer? (r-to-z Fisher transformation and statistical method?) Best regards, Matthieu

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Clusterwise correction for multiple comparisons
by Gwang-Won Kim 04 Sep '19

04 Sep '19

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-conform option in mri_convert produces crazy artefacts
by Rovai Antonin 04 Sep '19

04 Sep '19

External Email - Use Caution Hello again I have the following issue when running mri_convert. When using the option -conform option (as in the reconall pipeline), the sag slices seems to be shifted at some point (see attached pictures). What is happening? By the way the option description is not super clear, could you please give some extra details? Best Antonin [cid:6517702D-5283-43A2-9829-E5FA475ABA23@erasme.ulb.ac.be][cid:BD0A0CE3-A403-4733-9BDC-B38AEED75225@erasme.ulb.ac.be] [Hôpital Erasme] Lien vers Disclaimer<http://www.erasme.ulb.ac.be/email-disclaimer>

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

03 Sep '19

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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

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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>

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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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Freesurfer September 2019