External Email - Use Caution Thanks, Tim for your reply.
No, there is only "lh.pial" file exists not 'lh.pial_lgi. What might be the problem? Any help would be appreciated Thanks & regards -Korann On Sat, Jul 6, 2019 at 9:30 PM <freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer@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-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: [External] Re: rostral anterior cingulate fix? > (Zeng,Victor (BIDMC - Psychiatry)) > 2. Re: [External] Re: rostral anterior cingulate fix? (Bruce Fischl) > 3. Re: recon-all Error : inputs cannot have multiple frames. > ( Yueming ) > 4. Re: recon-all Error : inputs cannot have multiple frames. > (Bruce Fischl) > 5. error while running pial_lgi for gyrification index > (vittal korann) > 6. Re: error while running pial_lgi for gyrification index > (Tim Sch?fer) > 7. Viewing Uncorrected Significance Map in Freeview (Marie Hill) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 5 Jul 2019 17:42:28 +0000 > From: "Zeng,Victor (BIDMC - Psychiatry)" <vz...@bidmc.harvard.edu> > Subject: Re: [Freesurfer] [External] Re: rostral anterior cingulate > fix? > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <1562348548910.95...@bidmc.harvard.edu> > Content-Type: text/plain; charset="iso-8859-1" > > > Sorry, I thought I attached something > Victor Zeng > Beth Israel Deaconess Medical Center > Keshavan Lab > ph: 617 754 1237 > -- > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl < > fis...@nmr.mgh.harvard.edu> > Sent: Friday, July 5, 2019 10:24 AM > To: Freesurfer support list > Subject: [External] Re: [Freesurfer] rostral anterior cingulate fix? > > Hi Victor > > can you render the parcellation in that area on the surface (in freeview) > and show it to us? > > cheers > Bruce > > > On Fri, 5 Jul 2019, Zeng,Victor (BIDMC - Psychiatry) wrote: > > > > > Hi Freesurfer group - > > > > > > I'm using FS6.0 dev-20190118, and I'm processing a few brain scans. I'm > seeing a misparcellation of > > the right rostral anterior cingulate using tkmedit (I know tkmedit is > sorta deprecated), and it > > doesn't seem inappropriate to use control point fixes. How would you > best fix this (I'm open to > > using freeview), without just editing the aparc+aseg.mgz? > > > > > > Victor Zeng > > Beth Israel Deaconess Medical Center > > Keshavan Lab > > ph: 617 754 1237 > > -- > > > > > ____________________________________________________________________________________________________ > > > > This message is intended for the use of the person(s) to whom it may be > addressed. It may contain > > information that is privileged, confidential, or otherwise protected > from disclosure under > > applicable law. If you are not the intended recipient, any > dissemination, distribution, copying, or > > use of this information is prohibited. If you have received this message > in error, please > > permanently delete it and immediately notify the sender. Thank you. > > > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: Screenshot from 2019-07-05 13-41-46.png > Type: image/png > Size: 41889 bytes > Desc: Screenshot from 2019-07-05 13-41-46.png > Url : > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190705/626cd039/attachment-0001.png > > ------------------------------ > > Message: 2 > Date: Fri, 5 Jul 2019 13:45:40 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] [External] Re: rostral anterior cingulate > fix? > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.20.1907051345020....@door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > you did, but not a surface rendering. Load it with freeview and show it as > a surface (maybe inflated and white) > > On Fri, 5 Jul 2019, Zeng,Victor (BIDMC > - Psychiatry) wrote: > > > > > Sorry, I thought I attached something > > Victor Zeng > > Beth Israel Deaconess Medical Center > > Keshavan Lab > > ph: 617 754 1237 > > -- > > > > ________________________________________ > > From: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl < > fis...@nmr.mgh.harvard.edu> > > Sent: Friday, July 5, 2019 10:24 AM > > To: Freesurfer support list > > Subject: [External] Re: [Freesurfer] rostral anterior cingulate fix? > > > > Hi Victor > > > > can you render the parcellation in that area on the surface (in freeview) > > and show it to us? > > > > cheers > > Bruce > > > > > > On Fri, 5 Jul 2019, Zeng,Victor (BIDMC - Psychiatry) wrote: > > > >> > >> Hi Freesurfer group - > >> > >> > >> I'm using FS6.0 dev-20190118, and I'm processing a few brain scans. I'm > seeing a misparcellation of > >> the right rostral anterior cingulate using tkmedit (I know tkmedit is > sorta deprecated), and it > >> doesn't seem inappropriate to use control point fixes. How would you > best fix this (I'm open to > >> using freeview), without just editing the aparc+aseg.mgz? > >> > >> > >> Victor Zeng > >> Beth Israel Deaconess Medical Center > >> Keshavan Lab > >> ph: 617 754 1237 > >> -- > >> > >> > ____________________________________________________________________________________________________ > >> > >> This message is intended for the use of the person(s) to whom it may be > addressed. It may contain > >> information that is privileged, confidential, or otherwise protected > from disclosure under > >> applicable law. If you are not the intended recipient, any > dissemination, distribution, copying, or > >> use of this information is prohibited. If you have received this > message in error, please > >> permanently delete it and immediately notify the sender. Thank you. > >> > >> > > > ------------------------------ > > Message: 3 > Date: Sat, 6 Jul 2019 10:36:28 +0800 > From: " Yueming " <1028551...@qq.com> > Subject: Re: [Freesurfer] recon-all Error : inputs cannot have > multiple frames. > To: " freesurfer " <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <tencent_1282426509f1fbabd7c044c444a589bb2...@qq.com> > Content-Type: text/plain; charset="iso-8859-1" > > External Email - Use Caution > > My command: recon-all -all -i /usr/local/110/UN18/1.DCM -s 18p > I DON'T KNOW,WHAT KIND OF frames will be considered unmultiple? > My inputs' format is dicom,when it is about 200kB,the software can run and > has no such error.but when the dicom is more than 500kB,the next error will > happen: > > > > > Checking for (invalid) multi-frame inputs... > ERROR: input(s) cannot have multiple frames! > /usr/local/freesurfer/subjects/18/mri/orig/001.mgz has 17 frames > > > > My English is so bad that you know...... Forgive me,please! > > > WISH TO YOUR TEACHING AND REPLY. > > >From a graduate student of China Liaoning University . > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190706/560e6132/attachment-0001.html > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: not available > Type: image/jpeg > Size: 14156 bytes > Desc: not available > Url : > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190706/560e6132/attachment-0001.jpe > > ------------------------------ > > Message: 4 > Date: Fri, 5 Jul 2019 22:42:30 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] recon-all Error : inputs cannot have > multiple frames. > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.20.1907052241330....@door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="iso-8859-1" > > I think the dicom series that 1.DCM is part of is not a 3D T1-weighted > structural. Can you run mri_info on it, or dcmdump (or both)? > On Sat, 6 Jul > 2019, Yueming wrote: > > > > > ????????External Email - Use Caution???????? > > > > My command: recon-all -all -i /usr/local/110/UN18/1.DCM -s 18p? > > I DON'T KNOW,WHAT KIND OF frames will be considered unmultiple? > > My inputs' format is dicom,when it is about 200kB,the software can run > and has no such error.but > > when the dicom is more than 500kB,the next error will happen: > > > > [IMAGE] > > Checking for (invalid) multi-frame inputs... > > ERROR: input(s) cannot have multiple frames! > > /usr/local/freesurfer/subjects/18/mri/orig/001.mgz has 17 frames > > > > My English is so bad that you know......? Forgive me,please! > > > > WISH TO YOUR TEACHING AND REPLY. > > From a graduate student?of China Liaoning University .? > > > > > > ------------------------------ > > Message: 5 > Date: Sat, 6 Jul 2019 16:57:28 +0530 > From: vittal korann <vittalkor...@gmail.com> > Subject: [Freesurfer] error while running pial_lgi for gyrification > index > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > < > cacymot1cw-ws37dhyamo1wtf4np-v1ov0mmy6mjeavtk3pv...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi FS experts, > > I wanted to run the gyrification index for all patients with Schizophrenia > and volunteers. When I entered the command: > "recon-all -s SATM124 -qcache -measure pial_lgi" and the terminal output > > " Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects > Actual FREESURFER_HOME /usr/local/freesurfer > -rw-rw-r-- 1 root 1590 1054464 Jul 6 16:02 > /usr/local/freesurfer/subjects/SATM124/scripts/recon-all.log > Linux naren123 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6 12:03:31 > UTC 2019 x86_64 x86_64 x86_64 GNU/Linux > '/usr/local/freesurfer/bin/recon-all' -> > '/usr/local/freesurfer/subjects/SATM124/scripts/recon-all.local-copy' > #-------------------------------------------- > #@# Qdec Cache preproc lh pial_lgi fsaverage Sat Jul 6 16:39:03 IST 2019 > /usr/local/freesurfer/subjects/SATM124/surf > > mris_preproc --s SATM124 --hemi lh --meas pial_lgi --target fsaverage > --out lh.pial_lgi.fsaverage.mgh > > nsubjects = 1 > ERROR: cannot find /usr/local/freesurfer/subjects/SATM124/surf/lh.pial_lgi > Linux naren123 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6 12:03:31 > UTC 2019 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s SATM124 exited with ERRORS at Sat Jul 6 16:39:03 IST 2019 > > For more details, see the log file > /usr/local/freesurfer/subjects/SATM124/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting"; > > I never faced this problem before while running gyrification index. To me, > it's looks bizarre. > Would appreciate any help. > > Thanks & regards > -Korann > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190706/684397d5/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Sat, 6 Jul 2019 14:02:03 +0200 (CEST) > From: Tim Sch?fer <ts...@rcmd.org> > Subject: Re: [Freesurfer] error while running pial_lgi for > gyrification index > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <1748678951.441799.1562414523...@ox.hosteurope.de> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Just to be sure: *does* > /usr/local/freesurfer/subjects/SATM124/surf/lh.pial_lgi exist? > > Tim > > > On July 6, 2019 at 1:27 PM vittal korann <vittalkor...@gmail.com> wrote: > > > > > > External Email - Use Caution > > > > Hi FS experts, > > > > I wanted to run the gyrification index for all patients with > Schizophrenia > > and volunteers. When I entered the command: > > "recon-all -s SATM124 -qcache -measure pial_lgi" and the terminal > output > > > > " Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > > Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects > > Actual FREESURFER_HOME /usr/local/freesurfer > > -rw-rw-r-- 1 root 1590 1054464 Jul 6 16:02 > > /usr/local/freesurfer/subjects/SATM124/scripts/recon-all.log > > Linux naren123 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6 > 12:03:31 > > UTC 2019 x86_64 x86_64 x86_64 GNU/Linux > > '/usr/local/freesurfer/bin/recon-all' -> > > '/usr/local/freesurfer/subjects/SATM124/scripts/recon-all.local-copy' > > #-------------------------------------------- > > #@# Qdec Cache preproc lh pial_lgi fsaverage Sat Jul 6 16:39:03 IST 2019 > > /usr/local/freesurfer/subjects/SATM124/surf > > > > mris_preproc --s SATM124 --hemi lh --meas pial_lgi --target fsaverage > > --out lh.pial_lgi.fsaverage.mgh > > > > nsubjects = 1 > > ERROR: cannot find > /usr/local/freesurfer/subjects/SATM124/surf/lh.pial_lgi > > Linux naren123 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6 > 12:03:31 > > UTC 2019 x86_64 x86_64 x86_64 GNU/Linux > > > > recon-all -s SATM124 exited with ERRORS at Sat Jul 6 16:39:03 IST 2019 > > > > For more details, see the log file > > /usr/local/freesurfer/subjects/SATM124/scripts/recon-all.log > > To report a problem, see > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting"; > > > > I never faced this problem before while running gyrification index. To > me, > > it's looks bizarre. > > Would appreciate any help. > > > > Thanks & regards > > -Korann > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Dr. Tim Sch?fer > Postdoc Computational Neuroimaging > Department of Child and Adolescent Psychiatry, Psychosomatics and > Psychotherapy > University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany > > > > ------------------------------ > > Message: 7 > Date: Sat, 6 Jul 2019 13:38:54 +0000 > From: Marie Hill <marie_h...@outlook.com> > Subject: [Freesurfer] Viewing Uncorrected Significance Map in Freeview > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > < > lnxp123mb1817d23ee50cb4f16728a2e0f0...@lnxp123mb1817.gbrp123.prod.outlook.com > > > > Content-Type: text/plain; charset="iso-8859-1" > > External Email - Use Caution > > Hi everyone, > > > I have just finished running glmfit. When I try to load the significance > maps in freeview, they appear to load for a moment and then disappear, just > showing the brain volume without any highlighted areas of significance. > Does anyone have any idea why this could be? > > > I ran the command: freeview -f > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.g4v1.glmdir/bipolar-vs-schizophrenia/sig.mgh:overlay_threshold=4,5 > -viewport 3d > > > Kindest Regards, > > > Marie > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20190706/15f4b7fd/attachment-0001.html > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 185, Issue 9 > ****************************************** >
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