External Email - Use Caution Dear Doug,
Unfortunately I don't see your response to my email though there is a Re:"my subject" at the beginning. Get Outlook for iOS<https://aka.ms/o0ukef> ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of freesurfer-requ...@nmr.mgh.harvard.edu <freesurfer-requ...@nmr.mgh.harvard.edu> Sent: Tuesday, October 27, 2020 6:48:06 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Freesurfer Digest, Vol 200, Issue 55 Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=trt-sjpFDcQer0uPbrT73RkJnjuD1E1J9roqMEob-KQ&s=f80iTunbBiin4RJydjrD3YmFUgwlaRFK0JukEYtVqSE&e= 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. Re: Convert FSL .nii ROI into FreeSurfer Label (Douglas N. Greve) 2. Re: Fwd: Freesurfer edits (Douglas N. Greve) 3. Re: Please help me. Stuck with this for too long!!! (Douglas N. Greve) 4. Re: question about PETSurfer (Douglas N. Greve) 5. Re: Issues with Surface segmentation (Sierra Ann R. Jarvis) ---------------------------------------------------------------------- Message: 1 Date: Tue, 27 Oct 2020 18:05:37 -0400 From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> Subject: Re: [Freesurfer] Convert FSL .nii ROI into FreeSurfer Label To: <freesurfer@nmr.mgh.harvard.edu> Message-ID: <6b459e19-c830-eda7-d365-484a77ca3...@mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" A surface label or a volume label? On 10/25/2020 2:17 PM, Hua, Jessica wrote: > > ????????External Email - Use Caution > > Hi FreeSurfer Experts, > > How can I convert a .nii ROI into a FreeSurfer label? I was able to > convert the .nii into a .mgh file but could not figure out how to > convert to a label file. > > Thank you, > > Jessica > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=trt-sjpFDcQer0uPbrT73RkJnjuD1E1J9roqMEob-KQ&s=f80iTunbBiin4RJydjrD3YmFUgwlaRFK0JukEYtVqSE&e= -------------- next part -------------- An HTML attachment was scrubbed... URL: https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201027_1d7f413f_attachment-2D0001.html&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=trt-sjpFDcQer0uPbrT73RkJnjuD1E1J9roqMEob-KQ&s=okbqKiiSu5HY3lZc8ni-pCiuG0qOwS-0LT-Ev3xZDAs&e= ------------------------------ Message: 2 Date: Tue, 27 Oct 2020 18:07:08 -0400 From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> Subject: Re: [Freesurfer] Fwd: Freesurfer edits To: <freesurfer@nmr.mgh.harvard.edu> Message-ID: <008c362b-b754-25c7-a894-34f0bac41...@mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" It looks like the image darkens a lot at the top. Try putting control points in the WWM near the start of the gyrus. make sure they are truly in WM! On 10/25/2020 9:03 PM, Alexopoulos, Dimitrios wrote: > > ????????External Email - Use Caution > > Any comments from FS users to best best tackle these manual edits? > > Jim > > Get Outlook for Android > <https://urldefense.proofpoint.com/v2/url?u=https-3A__aka.ms_ghei36&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=trt-sjpFDcQer0uPbrT73RkJnjuD1E1J9roqMEob-KQ&s=-Swvhk8ADKQO3RtpP9UBhpvaLaWjyhTmVT0kTd1LucQ&e= > > > > ------------------------------------------------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alexopoulos, > Dimitrios <dimitriosalexopou...@wustl.edu> > *Sent:* Tuesday, October 20, 2020, 10:25 AM > *To:* Freesurfer support list > *Subject:* [Freesurfer] Freesurfer edits > > ** External Email - Caution ** > > ????????External Email - Use Caution > > Hi freesurfer editing experts. > > Below are snapshots of the brainmask, aseg and wm.mgz for a 2 year old > run through FS 7.1.1 > > I?m hoping for feedback on the best way to make the relevant edits to > the three blue-circled regions. > > 1.In the superior regions I think control points will help to pick up > some WM to help fuill > > 2.In the left hemisphere medial prefrontal (gyrus rectus) regions, the > WM is overestimated. I presume removing WM voxels from the wm.mgz is > the best approach? > > 3.The left temporal pole region is missing GM/cortex and there really > isn?t any WM that would help with controls points or adding WM voxels. > How can I add GM to this area? > > ------------------------------------------------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. If you have > received this email in error, please immediately notify the sender via > telephone or return mail. > > > ------------------------------------------------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. 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Name: image010.jpg Type: image/jpeg Size: 20555 bytes Desc: not available Url : https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201027_812688d5_attachment-2D0007.jpg&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=trt-sjpFDcQer0uPbrT73RkJnjuD1E1J9roqMEob-KQ&s=nHSjtzEHShtJST7G9ESjExAmcjKokA2J-rBF78zuflg&e= ------------------------------ Message: 3 Date: Tue, 27 Oct 2020 18:11:14 -0400 From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> Subject: Re: [Freesurfer] Please help me. Stuck with this for too long!!! To: <freesurfer@nmr.mgh.harvard.edu> Message-ID: <dfef1cd8-f0a6-ad83-6793-7a7cbff5d...@mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" On 10/26/2020 3:58 PM, Basavaraju, Rakshathi wrote: > > ????????External Email - Use Caution > > Dear Freesurfer team, > > I have been trying to extract local gyrification index in a dataset > according to a label which I have created. > > 1) First of all, I extracted lGI as per DKT areas, which one is lGI > value in the ?h.pial_lgi.stats file (derived on running a lGI recon?) > > # ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd > MeanCurv GausCurv FoldInd CurvInd > caudalanteriorcingulate ? ? ? ? ? ? ? ? ?1094 ? ?774 ? 2285 ?3.234 > 0.889 ? ? 0.129 ? ? 0.031 ? ? ? 15 ? ? 1.3 > > Is the lGI of caudal anterior cingulate 3.234 or 1.3? It is 3.234 > > 2) I could register a label which I have created to the surface of > individual subjects using mrilabel2label which ran alright, and I > could view the label on the surface of the individual subject intact > on freeview. But after that I am unable to extract lGI value from the > designated label only using mris_anatomicalstats. > > I used the following command:?mris_anatomical_stats -l > label/outlabelbase-0001.label -f stats/occipital_lGI.stats > FS6-LGI-05-Feb-2020_schiz018_G1_MPRAGE rh pial_lgi > > This throws the error:?#MRISread: file > '/mnt/share/projects/provenzano/Human/CHR_Rakshathi/LGI/FS6-LGI-05-Feb-2020_schiz018_G1_MPRAGE/surf/rh.pial_lgi' > has many more faces than vertices! > Probably trying to use a scalar data file as a surface! Try using mri_segstsats, like mri_segstats --slabel subject rh? label/outlabelbase-0001.label --id 1 --o mean.dat > > Then I converted rh_pial.lgi to rh_pial.lgi.asc:?mris_convert -c > rh.pial_lgi rh.white rh.pial_lgi.asc > and then ran: mris_anatomical_stats -l label/outlabelbase-0001.label > -f stats/occipital_lGI.stats FS6-LGI-05-Feb-2020_schiz018_G1_MPRAGE rh > pial_lgi.asc > > then the error:?Segmentation fault (core dumped) > > Kindly help me, this analysis is way overdue, and it is seeming like > an endless tunnel only of new errors.... > > > > > > Dr. Rakshathi Basavaraju (MD Psychiatry) > Postdoctoral Research Scientist > Taub Institute for Research on Alzheimer's Disease and the Aging Brain > Columbia University Medical Centre > 622 West, 168th Street, New York - 10032 > E-Mail: rb3...@cumc.columbia.edu <mailto:rb3...@cumc.columbia.edu> > _https://urldefense.proofpoint.com/v2/url?u=https-3A__indiaalliance.org_fellow_rakshathi-2Dbasavaraju-5F&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=trt-sjpFDcQer0uPbrT73RkJnjuD1E1J9roqMEob-KQ&s=0ATE5cWQpQoANHkhyGjkWNs_uH17WNjvGqEgD8QmROE&e= > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=trt-sjpFDcQer0uPbrT73RkJnjuD1E1J9roqMEob-KQ&s=f80iTunbBiin4RJydjrD3YmFUgwlaRFK0JukEYtVqSE&e= -------------- next part -------------- An HTML attachment was scrubbed... URL: https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201027_e4b1ad02_attachment-2D0001.html&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=trt-sjpFDcQer0uPbrT73RkJnjuD1E1J9roqMEob-KQ&s=fdlswRxbUJfsW5HaRVms6JiLupRXSxFHVv1zGhvFf7E&e= ------------------------------ Message: 4 Date: Tue, 27 Oct 2020 18:14:45 -0400 From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> Subject: Re: [Freesurfer] question about PETSurfer To: <freesurfer@nmr.mgh.harvard.edu> Message-ID: <b36826c6-2066-9aa6-ac23-0100789e1...@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" as you note, the gtmseg.mgz has higher resolution and several new ROIs. the higher res is for partial volume correction. The inclusion of pons to for the possibility of using it as a reference region, which often happens in AD studies of FDG. Vermis is for use in serotonin studies so it can be excluded from the rest of cerebellar cortex as vermis might have some receptors there making is inappropriate to use as a reference region. On 10/26/2020 9:55 PM, ??? wrote: > > ????????External Email - Use Caution > > Hello Freesurfer Developers, > > I have some questions about why the first step of PETSurfer needs to > create gtmseg.mgz segmentation. > > I noticed that the differences between gtmseg.mgz and aseg.mgz are the > gtmseg.mgz has a higher resolution and also to separate the pons and > the vermis from the brainstem and the cerebellar. I would like to know > whether the reason to create the gtmseg.mgz segmentation is because > the ROI is based on the Pons? > If so, I also have read some other articles that the ROI is based in > other regions. Why does the Freesurfer choose Pons instead? Also, what > is the purpose of separating the vermis from the cerebellar? Is the > reason to create the gtmseg.mgz segmentation just for the system to > run the PVC? > > looking forward to your reply. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=trt-sjpFDcQer0uPbrT73RkJnjuD1E1J9roqMEob-KQ&s=f80iTunbBiin4RJydjrD3YmFUgwlaRFK0JukEYtVqSE&e= -------------- next part -------------- An HTML attachment was scrubbed... URL: https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201027_9fe79deb_attachment-2D0001.html&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=trt-sjpFDcQer0uPbrT73RkJnjuD1E1J9roqMEob-KQ&s=8oHXXJaymD0uUS4Dl8_-Z04x0eLrGY_5NFgjR9sSxjI&e= ------------------------------ Message: 5 Date: Tue, 27 Oct 2020 16:48:01 -0600 From: "Sierra Ann R. Jarvis" <jarvis.sier...@gmail.com> Subject: Re: [Freesurfer] Issues with Surface segmentation To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <0f1d5bca-b2ee-4759-984a-2a707402a...@gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi! So, basically what is happening is the white matter and pial surfaces are not aligning up correctly on any of the slices. The white matter surface isn?t outlining white matter, which is causing the pial to not outline the pial. It almost looks like the pial is outlining the wm surface that is how off it is. The aseg.mgz is just as bad. I converted the imagine to a pdf hopefully you can view it better. On Tue, Oct 27, 2020 at 4:05 PM Douglas N. Greve <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: It is a little hard to see what is going on, but the image looks pretty blurry. How does the aseg.mgz look? On 10/24/2020 2:33 PM, Sierra Ann Jarvis wrote: > External Email - Use Caution > > Hello FreeSurfer Developers, > > I am attempting to run this subject through a longitudinal process. I have > successfully ran and edited the cross-sectional and the .base. My problem > occurs when I run the .longs. I do not receive an error in the recon-all.log, > but the surfaces on the image when I pull it up on FreeView are very jumbled. > Below I have attached a screenshot of a coronal slice to give you an idea of > what I am dealing with. > > I ran the subject through: recon-all -long sub_post/ sub.base -all > > > > FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > > Recon-all log last line: recon-all -s sub-5504_post.long.sub-5504.base > finished without error at Fri Oct 16 13:44:10 MDT 2020 > > > Thank you for your time, > Sierra Jarvis > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=trt-sjpFDcQer0uPbrT73RkJnjuD1E1J9roqMEob-KQ&s=f80iTunbBiin4RJydjrD3YmFUgwlaRFK0JukEYtVqSE&e= > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=trt-sjpFDcQer0uPbrT73RkJnjuD1E1J9roqMEob-KQ&s=f80iTunbBiin4RJydjrD3YmFUgwlaRFK0JukEYtVqSE&e= > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=trt-sjpFDcQer0uPbrT73RkJnjuD1E1J9roqMEob-KQ&s=f80iTunbBiin4RJydjrD3YmFUgwlaRFK0JukEYtVqSE&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=trt-sjpFDcQer0uPbrT73RkJnjuD1E1J9roqMEob-KQ&s=f80iTunbBiin4RJydjrD3YmFUgwlaRFK0JukEYtVqSE&e= > -------------- next part -------------- An HTML attachment was scrubbed... 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