External Email - Use Caution Re:"Re: [Freesurfer] Creating ROI from sig.mgh"
Dear Douglas, Do you recommend running mri_glmfit-sim on each individual subject? I have a significant cluster in sig.mgh derived out of a contrast involving many subjects in vertex-based lgi analysis. Now I want an ROI out of the significant cluster (p<0.001 uncorrected) and extract lGI values from this created ROI from each subject. 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://indiaalliance.org/fellow/rakshathi-basavaraju ________________________________ 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 20, 2020 2:32 AM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Freesurfer Digest, Vol 200, Issue 36 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=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=tG1_CQT5xYnSGjTRQbiit6JICsXOxsYXs3ROpbZA_w8&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: Problem of the Mapping Label to the Subject (Douglas N. Greve) 2. Re: Creating ROI from sig.mgh (Douglas N. Greve) 3. Re: Problem of the Mapping Label to the Subject (Wang, Ruopeng) 4. Re: Problem of the Mapping Label to the Subject (???) 5. fwhm values for gyrification index analysis (vittal korann) 6. Tracula error: run list is longer than subject list (Shanika Jayakody) 7. Re: Exited with errors, segmentation fault (Hoopes, Andrew) 8. mkanalysis-sess and mkcontrast-sess scripts for FIR analysis (Fang, Angela,Ph.D.) 9. Re: surf pial_lgi not created in version 7.1.0 (Kathy L. Pearson) 10. Re: Tracula error: run list is longer than subject list (Yendiki, Anastasia) 11. replace the vertex_label_index in .annot file ( 1248742467 ) 12. why can't I receive a reply from others in my mailbox? ( 1248742467 ) 13. Statistic Difference Region on the Fsaverage Turned into No Statistic Difference after Mapping onto the Subjects (???) 14. Problem with dcmunpack on freesurfer (Praveen Raghunathan) 15. Error during skullstripping: numerical result out of range (Hye Min Shin) 16. Re: Problem with dcmunpack on freesurfer (fsbuild) ---------------------------------------------------------------------- Message: 1 Date: Mon, 19 Oct 2020 12:22:50 -0400 From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> Subject: Re: [Freesurfer] Problem of the Mapping Label to the Subject To: <freesurfer@nmr.mgh.harvard.edu> Message-ID: <16e556fb-a4e8-01b4-87fe-15d672cd6...@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" There is no QDEC in 7.X, we have abandoned it. On 10/19/2020 11:09 AM, ??? wrote: > > ????????External Email - Use Caution > > Thanks for your help, I have tried FS 7.1.1, while there is no Qdec > command when I tried FS 7.1.1 in the terminal window. How should I > start the Qdec in the 7.1.1 version. > > Best wishes > Mengjun Li > > > > -----????----- > *???:*"Wang, Ruopeng" <rwa...@mgh.harvard.edu> > *????:*2020-10-19 21:07:45 (???) > *???:* "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > *??:* > *??:* Re: [Freesurfer] Problem of the Mapping Label to the Subject > > I think this is a bug in freeview from FS 6.0.0 that has been > fixed in 7.x. Would it be possible for you to try FS 7.1.1? A > quick workaround you may try first is to change the offset for the > inflated surface to 0 0 0 in freeview 6.0.0. > > Best, > Ruopeng > >> On Oct 19, 2020, at 2:38 AM, ??? <meng...@csu.edu.cn >> <mailto:meng...@csu.edu.cn>> wrote: >> >> ????????External Email - Use Caution >> >> >> >> >> >> Dear FreeSurfer Developers: >> >> My name is Mengjun Li, I am a MD in the Second Xiangya >> Hospital, Central South University. I compared the cortex, >> area, volume in the mild traumatic brain injury patients with >> health control by the FreeSurFer and found the problem when >> mapping label to the single subjects. >> >> There is statistic difference in the area and volume >> between?the mild traumatic brain injury patients and the >> health control, I defined the?statistic difference region as >> a label on the fsaverage and mapped this label to subjects by >> the Qdec. Although the label defined on the fsaverage was >> mapped onto all subjects successfully,the label in the >> subjects did not match well with the inflated cortex of the >> subjects. At the same time, the volume and area value of the >> label have been extracted in every subject and I found that >> there is no statistic difference between the mild traumatic >> brain injury patients and health control. I have checked the >> segmentation of every subjects and it was a good job done by >> FreeSurFer. Attached figures illustrated the label mapping >> results. >> >> Figure 1: the label defined on the fsaverage >> Figure 2: the lateral view of the label in the subjects >> Figure 3: the inferior view of the label in the subjects >> >> FreeSurfer >> version:?freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c >> Platform: macOS High Sierra >> >> I am sending this email for help since I am not sure how to >> fix this problem. Looking forward to hearing your reply! >> Thank you very much! >> >> Best wishes >> Mengjun Li >> Second Xiangya Hospital >> Central South University. >> >> >> >> >> >> <Figure 1.png><Figure 2.png><Figure >> 3.png>_______________________________________________ >> 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=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=tG1_CQT5xYnSGjTRQbiit6JICsXOxsYXs3ROpbZA_w8&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=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=tG1_CQT5xYnSGjTRQbiit6JICsXOxsYXs3ROpbZA_w8&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_20201019_d71391e1_attachment-2D0001.html&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=-_uu7y0xbeuo3AZjIuqPtrjGLHNCMrVThxb5KMPO_fk&e= ------------------------------ Message: 2 Date: Mon, 19 Oct 2020 12:26:48 -0400 From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> Subject: Re: [Freesurfer] Creating ROI from sig.mgh To: <freesurfer@nmr.mgh.harvard.edu> Message-ID: <7984cce6-3e33-7681-64bf-07336a3a0...@mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" Try using the correction for multiple comparisons (mri_glmfit-sim). Set the CWP threshold to 1.0 to get all the clusters. It will create a table with GI values for each cluster. Run mri_glmfit-sim with --help and/or look on line to get more info On 10/14/2020 3:55 PM, Basavaraju, Rakshathi wrote: > > ????????External Email - Use Caution > > I have run a vertex based gyrification index analysis. Now I want to > create a mask/ROI from the cluster of vertices which are above the > threshold of 3 in sig.mgh file (p<0.001). Which command should I use > for this purpose? Is it mri_mask? or mri_vol2roi? > > Next how do I extract the GI value (a numeric) from the above obtained > ROI from individual scans? > > If anyone has done anything similar with thickness or volume (which I > am sure many would have done), it would be helpful if you guided me. > Eagerly waiting for your response. > > Thanks, > 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=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=U_esZjJrgdvHo23FGg4PZzhtM9I0SVSWUJLK8PFObL8&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=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=tG1_CQT5xYnSGjTRQbiit6JICsXOxsYXs3ROpbZA_w8&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_20201019_a9eb00f8_attachment-2D0001.html&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=wBWByytur1XOLnQXmuEyJaVJIlOXeTvH9gQM0_TRB9A&e= ------------------------------ Message: 3 Date: Mon, 19 Oct 2020 16:39:56 +0000 From: "Wang, Ruopeng" <rwa...@mgh.harvard.edu> Subject: Re: [Freesurfer] Problem of the Mapping Label to the Subject To: ??? <meng...@csu.edu.cn> Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <40df5eea-1ad2-4f1e-8356-ebb48b15c...@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Sorry I was commenting on the screenshots in your previous email. I thought they were from freeview. We do not support Qdec anymore in 7.x versions. Ruopeng On Oct 19, 2020, at 11:09 AM, ??? <meng...@csu.edu.cn<mailto:meng...@csu.edu.cn>> wrote: External Email - Use Caution Thanks for your help, I have tried FS 7.1.1, while there is no Qdec command when I tried FS 7.1.1 in the terminal window. How should I start the Qdec in the 7.1.1 version. Best wishes Mengjun Li -----????----- ???:"Wang, Ruopeng" <rwa...@mgh.harvard.edu<mailto:rwa...@mgh.harvard.edu>> ????:2020-10-19 21:07:45 (???) ???: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> ??: ??: Re: [Freesurfer] Problem of the Mapping Label to the Subject I think this is a bug in freeview from FS 6.0.0 that has been fixed in 7.x. Would it be possible for you to try FS 7.1.1? A quick workaround you may try first is to change the offset for the inflated surface to 0 0 0 in freeview 6.0.0. Best, Ruopeng On Oct 19, 2020, at 2:38 AM, ??? <meng...@csu.edu.cn<mailto:meng...@csu.edu.cn>> wrote: External Email - Use Caution Dear FreeSurfer Developers: My name is Mengjun Li, I am a MD in the Second Xiangya Hospital, Central South University. I compared the cortex, area, volume in the mild traumatic brain injury patients with health control by the FreeSurFer and found the problem when mapping label to the single subjects. There is statistic difference in the area and volume between the mild traumatic brain injury patients and the health control, I defined the statistic difference region as a label on the fsaverage and mapped this label to subjects by the Qdec. Although the label defined on the fsaverage was mapped onto all subjects successfully,the label in the subjects did not match well with the inflated cortex of the subjects. At the same time, the volume and area value of the label have been extracted in every subject and I found that there is no statistic difference between the mild traumatic brain injury patients and health control. I have checked the segmentation of every subjects and it was a good job done by FreeSurFer. Attached figures illustrated the label mapping results. Figure 1: the label defined on the fsaverage Figure 2: the lateral view of the label in the subjects Figure 3: the inferior view of the label in the subjects FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: macOS High Sierra I am sending this email for help since I am not sure how to fix this problem. Looking forward to hearing your reply! Thank you very much! Best wishes Mengjun Li Second Xiangya Hospital Central South University. <Figure 1.png><Figure 2.png><Figure 3.png>_______________________________________________ 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=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=tG1_CQT5xYnSGjTRQbiit6JICsXOxsYXs3ROpbZA_w8&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_20201019_0754a0c9_attachment-2D0001.html&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=__QAabx-VBJRCzjE3VVj-al0m5mIVXzEPc4s8JRqVmc&e= ------------------------------ Message: 4 Date: Tue, 20 Oct 2020 01:15:16 +0800 (GMT+08:00) From: ??? <meng...@csu.edu.cn> Subject: Re: [Freesurfer] Problem of the Mapping Label to the Subject To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>, rwa...@mgh.harvard.edu Message-ID: <30ff0034.15a74.17541dbaa23.coremail.meng...@csu.edu.cn> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Thank you very much, I will try surface analysis with command in 7.1.1 version -----????----- ???:"Wang, Ruopeng" <rwa...@mgh.harvard.edu> ????:2020-10-20 00:39:56 (???) ???: "???" <meng...@csu.edu.cn> ??: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> ??: Re: [Freesurfer] Problem of the Mapping Label to the Subject Sorry I was commenting on the screenshots in your previous email. I thought they were from freeview. We do not support Qdec anymore in 7.x versions. Ruopeng On Oct 19, 2020, at 11:09 AM, ??? <meng...@csu.edu.cn> wrote: External Email - Use Caution Thanks for your help, I have tried FS 7.1.1, while there is no Qdec command when I tried FS 7.1.1 in the terminal window. How should I start the Qdec in the 7.1.1 version. Best wishes Mengjun Li -----????----- ???:"Wang, Ruopeng" <rwa...@mgh.harvard.edu> ????:2020-10-19 21:07:45 (???) ???: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> ??: ??: Re: [Freesurfer] Problem of the Mapping Label to the Subject I think this is a bug in freeview from FS 6.0.0 that has been fixed in 7.x. Would it be possible for you to try FS 7.1.1? A quick workaround you may try first is to change the offset for the inflated surface to 0 0 0 in freeview 6.0.0. Best, Ruopeng On Oct 19, 2020, at 2:38 AM, ??? <meng...@csu.edu.cn> wrote: External Email - Use Caution Dear FreeSurfer Developers: My name is Mengjun Li, I am a MD in the Second Xiangya Hospital, Central South University. I compared the cortex, area, volume in the mild traumatic brain injury patients with health control by the FreeSurFer and found the problem when mapping label to the single subjects. There is statistic difference in the area and volume between the mild traumatic brain injury patients and the health control, I defined the statistic difference region as a label on the fsaverage and mapped this label to subjects by the Qdec. Although the label defined on the fsaverage was mapped onto all subjects successfully,the label in the subjects did not match well with the inflated cortex of the subjects. At the same time, the volume and area value of the label have been extracted in every subject and I found that there is no statistic difference between the mild traumatic brain injury patients and health control. I have checked the segmentation of every subjects and it was a good job done by FreeSurFer. Attached figures illustrated the label mapping results. Figure 1: the label defined on the fsaverage Figure 2: the lateral view of the label in the subjects Figure 3: the inferior view of the label in the subjects FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: macOS High Sierra I am sending this email for help since I am not sure how to fix this problem. Looking forward to hearing your reply! Thank you very much! Best wishes Mengjun Li Second Xiangya Hospital Central South University. <Figure 1.png><Figure 2.png><Figure 3.png>_______________________________________________ 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=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=tG1_CQT5xYnSGjTRQbiit6JICsXOxsYXs3ROpbZA_w8&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_20201020_aeb43cf9_attachment-2D0001.html&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=1KoHnErKMnm8lP-FxUiYJQeZZfYPuU9WK61NBAwmLUM&e= ------------------------------ Message: 5 Date: Mon, 19 Oct 2020 23:43:32 +0530 From: vittal korann <vittalkor...@gmail.com> Subject: [Freesurfer] fwhm values for gyrification index analysis To: "Douglas N. Greve" <dgr...@mgh.harvard.edu>, freesurfer@nmr.mgh.harvard.edu Message-ID: <CACyMoT1N-q5Mmkkmr=m_x1ue+4e5bmhenqvsjsr99xhrb7-...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi Doug I'm analyzing the gyrification values between schizophrenia and healthy volunteers. While performing group analysis in QDEC, I encountered an error when setting the smoothing (fwhm) parameter to 25. Here is the error message from the terminal output > fwhm.dat: 66.612034, rounded to 67 > ERROR: fwhm out-of-range (< 1 or > 30)! > Error in Monte Carlo simulation: Error running mri_surfcluster! The same error persists for all smoothing values i.e. 5,10,15,20,25. QDEC works when I set fwhm to zero units. Why it is like this? And what is the ideal value of smoothing kernel (fwhm) for gyrification analysis? With thanks Korann -------------- 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_20201019_35aa521d_attachment-2D0001.html&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=cgBfUzBhUVrY9e9ZqChJSptZh3PJGSQvPvKViNrhtDo&e= ------------------------------ Message: 6 Date: Mon, 19 Oct 2020 18:43:33 +0000 From: Shanika Jayakody <shanika.jayak...@einsteinmed.org> Subject: [Freesurfer] Tracula error: run list is longer than subject list To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Message-ID: <cy4pr08mb2374ece1695972186120f1b696...@cy4pr08mb2374.namprd08.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" External Email - Use Caution Hello, I have been trying to run trac-all on a DWI of a participant, but I keep getting the error "run list is longer than subject list" I have created a configuration file setting sublist and runlist to just one subject so I am not sure what the error is about. I wonder if anyone can help me figure out a solution. Many thanks Oshadi -------------- 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_20201019_1d0bcf58_attachment-2D0001.html&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=VWdcQago6CZr5tZFfxKABCFs2tXMmrOommfhXLlFtbM&e= ------------------------------ Message: 7 Date: Mon, 19 Oct 2020 22:17:50 +0000 From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu> Subject: Re: [Freesurfer] Exited with errors, segmentation fault To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <c75378b1-8d53-44ea-a72b-a62f046a4...@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Julia, This is a small bug that's been fixed in the 7.1.1 patch release. I would recommend updating freesurfer versions (there will be no differences in recon-all results). Best, Andrew ?On 10/13/20, 8:44 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Julia Lam" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of julia....@mau.se> wrote: External Email - Use Caution Hi, In one of 56 volumes, recon-all exited with errors (segmentation fault). I tried to rerun but received the same result. How can this be solved? I?ve attached the recon-all.log and recon-all.error. I am looking forward to your reply. Kind regards, Julia Lam ------------------------------ Message: 8 Date: Mon, 19 Oct 2020 23:03:37 +0000 From: "Fang, Angela,Ph.D." <af...@mgh.harvard.edu> Subject: [Freesurfer] mkanalysis-sess and mkcontrast-sess scripts for FIR analysis To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Message-ID: <b8b37bfa-7cc6-4ff5-b3de-c182f8ce6...@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hello Freesurfer community, I am trying to configure first level FIR analyses and contrasts for an event related task based on the design in the attached paper. I have 3 conditions (self, other, case) plus fixation. I believe the time window is 30 sec with 11 frames, 12 time points and the TR = 2.5 sec: Timecourse: -5 -2.5 0 2.5 5 7.5 10 12.5 15 17.5 20 25 Timepoint: 0 1 2 3 4 5 6 7 8 9 10 11 The paradigm file for 1 of my 3 runs (attached) was developed using Optseq with Doug?s help, and I believe the TER in this case would be 2.5 sec. Do the following commands look correct? mkanalysis-sess -analysis selfotherfir.lh -TR 2.5 -refeventdur 2.5 -paradigm self.other.par -event-related -fsd bold -surface fsaverage lh -nconditions 3 -timewindow 30 -fir 5 30 -TER 2.5 -per-run mkcontrast-sess -analysis selfotherfir.lh -contrast self-v-other -a 1 -c 3 -no-sumdelays -rmprestim I want to be able to view timecourses at each time point (hence the -no-sumdelays flag) in tksurfer (or freeview) but I am not sure about using the -rmprestim flag. Is there any instance when I would not want to remove baseline shifts? Thanks for your help! Angela Angela Fang, Ph.D. Assistant Professor of Psychology, Harvard Medical School Department of Psychiatry, Massachusetts General Hospital OCD and Related Disorders Program 185 Cambridge Street, Suite 2000 Boston, MA 02114 Email: af...@mgh.harvard.edu<mailto:af...@mgh.harvard.edu> Phone: (617) 643-7717 Fax: (617) 643-3080 -------------- next part -------------- An HTML attachment was scrubbed... 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Name: Kelley_etal_JOCN_14.pdf Type: application/pdf Size: 190730 bytes Desc: Kelley_etal_JOCN_14.pdf Url : https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201019_37273bbd_attachment-2D0001.pdf&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=x1cogNNj21_vSYY2WhPlqLvedTTKlo2j390H9p8VcrY&e= ------------------------------ Message: 9 Date: Tue, 20 Oct 2020 00:24:36 +0000 From: "Kathy L. Pearson" <kathy.pear...@colorado.edu> Subject: Re: [Freesurfer] surf pial_lgi not created in version 7.1.0 To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Message-ID: <cy4pr03mb2774ea0d281b35a54bb2f5ca82...@cy4pr03mb2774.namprd03.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" External Email - Use Caution I am getting this error near the tail of the 7.1.0 recon-all.log file just before exit: ERROR: find_corresponding_center_FSformat did not complete successfully! At this link from May 13: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_freesurfer-40nmr.mgh.harvard.edu_msg66255.html&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=7MPLX2pP51-kEpKeS-bplvotLpYeWuycnnLm6THwRfE&e= I see that you have posted in reference to a similar question: https://urldefense.proofpoint.com/v2/url?u=https-3A__gate.nmr.mgh.harvard.edu_safelinks_greve_find-5Fcorresponding-5Fcenter-5FFSformat.m&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=PJzpdvS4af4z99W22MIzTO2rdu_jQL-hhhpgKvrhaLk&e= If this is different from the 7.1.0 distribution's file in the matlab directory May 11 10:04 find_corresponding_center_FSformat.m please let me know what authentication login/password combination is needed to access this to see if it will fix my errors. Is this file updated in the newer 7.1.1? Thanks, Kathy >Douglas N. Greve Mon, 19 Oct 2020 07:42:01 -0700 > Can you send the recon-all.log file? ______________________________________ From: Kathy L. Pearson <kathy.pear...@colorado.edu> Sent: Friday, October 9, 2020 10:47 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: surf pial_lgi not created in version 7.1.0 No, it does not exist, and my question is why not in 7.1.0 when it is created with the same two commands in 5.3.0? Thanks, Kathy > Douglas N. Greve Fri, 09 Oct 2020 05:49:32 -0700 > does that file exist? ________________________________________ From: Kathy L. Pearson Sent: Thursday, October 8, 2020 11:55 AM To: freesurfer@nmr.mgh.harvard.edu Subject: surf pial_lgi not created in version 7.1.0 In freesurfer version 5.3.0, I can successfully run: recon-all -autorecon-all -mprage -s $subj -qcache -localGI recon-all -s $subj -qcache -measure pial_lgi However, the same commands with 7.1.0 give an error after this last of a number of generated statements and no surf/*pial_lgi output: mris_preproc --s 147608 --hemi lh --meas pial_lgi --target fsaverage --out lh.pial_lgi.fsaverage.mgh nsubjects = 1 ERROR: cannot find subjects/147608/surf/lh.pial_lgi Is a new command needed for version 7.1.0? Thanks, Kathy Pearson ------------------------------ Message: 10 Date: Tue, 20 Oct 2020 00:33:16 +0000 From: "Yendiki, Anastasia" <ayend...@mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Message-ID: <mn2pr04mb5757a01add3e03b9b344a50a8a...@mn2pr04mb5757.namprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Make sure to use "subjlist", not "sublist". If that is not the issue, then please attach your log file and configuration file - it's hard to guess the issue without more information. Best, Anastasia. ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Shanika Jayakody <shanika.jayak...@einsteinmed.org> Sent: Monday, October 19, 2020 2:43 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Tracula error: run list is longer than subject list External Email - Use Caution Hello, I have been trying to run trac-all on a DWI of a participant, but I keep getting the error "run list is longer than subject list" I have created a configuration file setting sublist and runlist to just one subject so I am not sure what the error is about. I wonder if anyone can help me figure out a solution. Many thanks Oshadi -------------- 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_20201020_490cbd77_attachment-2D0001.html&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=Kd2_yWxOtP18sAQPMLB7aODkA5aQbUXOr1-KDmp5iGo&e= ------------------------------ Message: 11 Date: Tue, 20 Oct 2020 10:19:13 +0800 From: " 1248742467 " <1248742...@qq.com> Subject: [Freesurfer] replace the vertex_label_index in .annot file To: " freesurfer " <freesurfer@nmr.mgh.harvard.edu> Message-ID: <tencent_bfa3b22fce13ddfed68564c1fb5fe52dc...@qq.com> Content-Type: text/plain; charset="iso-8859-1" External Email - Use Caution hello, Previously, rh.white and rh.aparc.2009s.annot were used to generate vertex_id and vertex_label, ' from freesurfer_surface import Surface from freesurfer_surface import Label from freesurfer_surface import Annotation surface = Surface.read_triangular('rh.white') surface.load_annotation_file('rh.aparc.a2009s.annot') with open("rhlabels.txt","w") as f: for vertex_index, vertex in enumerate(surface.vertices): vertex_label_index = surface.annotation.vertex_label_index[vertex_index] vertex_label = surface.annotation.labels[vertex_label_index] #print(vertex_index, vertex, vertex_label) #f.write("vertex_index:{} vertexlabel:{} \n".format(vertex_index, vertex_label)) f.write("vertex_index:{} vertex_label:{}\n".format(vertex_index, vertex_label)) ' the output:vertex_index:0 vertexlabel:Label(name=S_precentral-sup-part, index=70, color=#1514c8) and the label_index obtained after a certain algorithm was updated to replace the vertex_labe_index in rh.aparc.2009s.annot, and then load the result with freeview. But I don't know how to replace the vertex_label_index value in .annot? -------------- 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_20201020_c2876ae3_attachment-2D0001.html&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=gcQleJGzMwXDdyxWEwZii5RUemu_2uAKYtiepFPKLgA&e= ------------------------------ Message: 12 Date: Tue, 20 Oct 2020 11:08:16 +0800 From: " 1248742467 " <1248742...@qq.com> Subject: [Freesurfer] why can't I receive a reply from others in my mailbox? To: " freesurfer " <freesurfer@nmr.mgh.harvard.edu> Message-ID: <tencent_8a82ff431e0cbc0cbbea7cc7ad779d461...@qq.com> Content-Type: text/plain; charset="iso-8859-1" External Email - Use Caution Hello, After i asked a question, why can't I receive a reply from others in my mailbox? -------------- 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_20201020_bf03c97f_attachment-2D0001.html&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=WnXgshZDdCeCXjVuEAH6sIQsIvowGF9ATdwBo4fYIM4&e= ------------------------------ Message: 13 Date: Tue, 20 Oct 2020 11:29:50 +0800 (GMT+08:00) From: ??? <meng...@csu.edu.cn> Subject: [Freesurfer] Statistic Difference Region on the Fsaverage Turned into No Statistic Difference after Mapping onto the Subjects To: freesurfer@nmr.mgh.harvard.edu, rwa...@mgh.harvard.edu Message-ID: <4f44b14a.15e80.175440e5129.coremail.meng...@csu.edu.cn> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Dear FreeSurfer Developers: I compared the thickness, area, volume in the mild traumatic brain injury patients with health control by FreeSurFer, and found a statistic difference region in the cortex area, I defined the statistic difference region as a label on the fsaverage and mapped this label to subjects by Qdec/mri_label2label. The label defined on the fsaverage was mapped onto all subjects successfully, and the label in subjects matched well with the inflated cortex of subjects in Freeview Then the area value of the label in every single subjects was extracted, and I found that there is no statistic difference in the area value between the mild traumatic brain injury patients and health control. I have checked the segmentation of every subjects and it was a good job done by FreeSurFer. FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform: macOS High Sierra. Best wishes Mengjun Li Second Xiangya Hospital Central South University -------------- 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_20201020_7d6f36c6_attachment-2D0001.html&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=UCygu1ItapB3kDDwYEAT8LRgYoJqQDJNY0HjNOYJ9z0&e= ------------------------------ Message: 14 Date: Tue, 20 Oct 2020 01:10:20 -0400 From: Praveen Raghunathan <praveenv...@gmail.com> Subject: [Freesurfer] Problem with dcmunpack on freesurfer To: freesurfer@nmr.mgh.harvard.edu Message-ID: <CAMjV3oiA-=OX=Xwwkgno6XsbGSuU7=fo6pjh-zbyhgbfg+m...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi Freesurfer developers, Sorry if I'm making a simple mistake that I've overlooked. I am currently trying to do the freesurfer tutorials available at https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu_fswiki_Tutorials&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=RzBPn0loh4mkCW_KW_t4m0WkJhPILHVXDIyRBEWJkg0&e= and am having problems with the dcmunpack command on freesurfer. Whenever I try to run the dcmunpack script (whether it's dcmunpack -help or dcmunpack -src . -scanonly scan.log), I get the following error message : bash: /home/praveen/freesurfer/bin/dcmunpack: /bin/tcsh: bad interpreter: No such file or directory I have installed freesurfer, added the license and am able to use freeview to open .mgz and .pial files so I'm not sure why dcmunpack is missing. I'm not able to find any online documentation on how to install or source that particular script either. I've searched the list archive and no similar errors have been reported. Please advise and let me know what I should do or what I'm doing wrong. I am currently running freesurfer on a virtual machine using Oracle Virtualbox 6.1 on my Windows laptop. The OS on the virtual machine I'm using is: Ubuntu 20.04.1 LTS and the freesurfer version is: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 I am using a Bash shell to run the commands. Thank you so much for your help! Please let me know if you need any other information. Sincerely Praveen V. Raghunathan -------------- 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_20201020_58cdb60d_attachment-2D0001.html&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=RlMu5AOeRQ8sdmIMcTzzyRpuXuTW9mqshU8lsytS9n8&e= ------------------------------ Message: 15 Date: Tue, 20 Oct 2020 14:13:12 +0900 From: Hye Min Shin <shinh...@bu.edu> Subject: [Freesurfer] Error during skullstripping: numerical result out of range To: freesurfer@nmr.mgh.harvard.edu Message-ID: <CADrX5GnGXPwjLy2qgwzjmwyKA=rkv9zbo3ujixcibko3uax...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi experts, While running recon-all on subjects with 3T T1 scans, I ran into an error with one subject during skullstripping stage. Recon-all was running with 3T flag. The error message is the following: register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=10.0 skull bounding box = (46, 56, 29) --> (216, 255, 255) using (103, 122, 142) as brain centroid... mean wm in atlas = 108, using box (82,97,114) --> (123, 146,169) to find MRI wm before smoothing, mri peak at 73 robust fit to distribution - 72 +- 7.4 distribution too broad for accurate scaling - disabling WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=100, mri_peak=108 after smoothing, mri peak at 0, scaling input intensities by inf Numerical result out of range I tried the following suggestion in https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_freesurfer-40nmr.mgh.harvard.edu_msg12605.html&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=PqX3Kr617qv2ZavVwa2emYljHtws5ewO5KwzdWf9a8w&e= but to no avail. It's just strange because only one subject has this issue and the subject's scan looks fine- no part of the brain seems cutoff. Any suggestions would be helpful. Best, Julia Shin -------------- 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_20201020_210d4cfc_attachment-2D0001.html&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=OWAnqitsJckcS0dT3GXdHAv5NTC8zjmv79EmYDUNPGI&e= ------------------------------ Message: 16 Date: Tue, 20 Oct 2020 08:31:56 +0200 From: fsbuild <fsbu...@contbay.com> Subject: Re: [Freesurfer] Problem with dcmunpack on freesurfer To: freesurfer@nmr.mgh.harvard.edu Cc: praveenv...@gmail.com Message-ID: <1603175516.5f8e845c7e...@trashmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello Praveen, The first line of dcmunpack script should indicate it calls the tcsh interpreter. However, neither csh or tcsh interpreters are installed by default on Ubuntu. The "which" command will probably report it is not found on your system thru your $PATH. $ which tcsh tcsh: Command not found But you can install the C shells manually via, $ sudo apt-get install tcsh csh .... after the install try the which command again. I am a working on a debian installer package so these manual installs will no longer be necessary. - R. On Oct 20, 2020, at 01:10, Praveen Raghunathan <praveenv...@gmail.com> wrote: External Email - Use Caution Hi Freesurfer developers,Sorry if I'm making a simple mistake that I've overlooked. I am currently trying to do the freesurfer tutorials available at https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu_fswiki_Tutorialsand&d=DwICAg&c=G2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U&r=4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo&m=O5u8mHb6nVxTU4xjRkLayq8Kra7qRgXg80IBVb6xw7w&s=XitTcEeCZFZQZIZDBP7w4RT3yQLMvV9WgE42KkCzK1w&e= am having problems with the dcmunpack command on freesurfer. Whenever I try to run the dcmunpack script (whether it's dcmunpack -help or dcmunpack -src . -scanonly scan.log), I get the following error message :bash: /home/praveen/freesurfer/bin/dcmunpack: /bin/tcsh: bad interpreter: No such file or directoryI have installed freesurfer, added the license and am able to use freeview to open .mgz and .pial files so I'm not sure why dcmunpack is missing. I'm not able to find any online documentation on how to install or source that particular script either. I've searched the list archive and no similar errors have been reported. Please advise and let me know what I should do or what I'm doing wrong.I am currently running freesurfer on a virtual machine using Oracle Virtualbox 6.1 on my Windows laptop. The OS on the virtual machine I'm using is:Ubuntu 20.04.1 LTS and the freesurfer version is: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551I am using a Bash shell to run the commands.Thank you so much for your help! Please let me know if you need any other information.SincerelyPraveen V. Raghunathan_______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... 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