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: rb3419@cumc.columbia.edumailto:rb3419@cumc.columbia.edu https://indiaalliance.org/fellow/rakshathi-basavaraju
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu freesurfer-request@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.ed... or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@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" dgreve@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-15d672cd645a@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" <RWANG4@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, RuopengOn Oct 19, 2020, at 2:38 AM, ??? <mengjun@csu.edu.cn <mailto:mengjun@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.ed...