Freesurfer

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Re: [Freesurfer] Bbregister misalignment {Disarmed}
by Douglas Greve 19 Jun '20

19 Jun '20

It might be a memory issue as you are converting a multi-frame volume to 256^3 float. Compute the memory needed to hold such a file and see if it exceeds the amount of memory on your computer On 6/18/20 11:36 AM, Mason Wells wrote: > > External Email - Use Caution > > Hi Doug, > > I got a killed message from this: > > mri_vol2vol --mov filtered_func_data.nii.gz --reg > partial-to-struct.lta --o movie-struct.nii.gz --fstarg > > regio_read_register: loading lta > > Matrix from regfile: > 0.96977 0.21949 0.10660 6.89014; > -0.10388 -0.02392 0.99430 -20.31174; > 0.22079 -0.97532 -0.00040 -13.45840; > 0.00000 0.00000 0.00000 1.00000; > > fstargfile orig.mgz > Using > /home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/mri/orig.mgz > as targ volume > movvol filtered_func_data.nii.gz > targvol > /home/masontwells/Documents/Data/freesurfer/subjects/MovPPT_001/mri/orig.mgz > outvol movie-struct.nii.gz > regfile partial-to-struct.lta > invert 0 > tal 0 > talres 2 > regheader 0 > noresample 0 > interp trilinear (1) > precision float (3) > Gdiag_no -1 > Synth 0 > SynthSeed 1592839527 > > Final tkRAS-to-tkRAS Matrix is: > 0.96977 0.21949 0.10660 6.89014; > -0.10388 -0.02392 0.99430 -20.31174; > 0.22079 -0.97532 -0.00040 -13.45840; > 0.00000 0.00000 0.00000 1.00000; > > > Vox2Vox Matrix is: > 0.32326 0.03553 -0.07316 -6.85702; > 0.07360 -0.00013 0.32511 -14.53098; > 0.03463 -0.33143 -0.00797 48.74134; > 0.00000 0.00000 0.00000 1.00000; > > /usr/local/freesurfer/bin/mri_vol2vol: line 3: 10135 Killed > mri_vol2vol.bin "$@" > > > *Mason T Wells, MSc* > > *PhD student* > > School of Optometry and Vision Sciences > > & Cardiff University Brain Research > > Imaging Centre (CUBRIC), School of Psychology > > Cardiff University > > Cardiff > > CF24 4HQ > > UK > > */Email/*: WellsMT1(a)cardiff.ac.uk <mailto:WellsMT1@cardiff.ac.uk> > > */Tel/*: 02920 879628 > > /*Web*/: Cardiff University webpage > <https://www.cardiff.ac.uk/people/research-students/view/974214-> > > > > *Mason T Wells, MSc* > > *Myfyriwr PhD* > > Yr Ysgol Optometreg a Gwyddorau’r Golwg > > & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr > Ysgol Seicoleg > > Prifysgol Caerdydd > > Heol Maindy > > Caerdydd > > CF24 4HQ > > DU > > */E-bost/*: WellsMT1(a)caerdydd.ac.uk <mailto:WellsMT1@caerdydd.ac.uk> > > */Ffôn/*: 02920 879628 > > > ------------------------------------------------------------------------ > *From:* Douglas N. Greve <dgreve(a)mgh.harvard.edu> > *Sent:* Thursday, June 18, 2020 4:21 PM > *To:* Mason Wells <WellsMT1(a)cardiff.ac.uk>; Freesurfer support list > <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] Bbregister misalignment {Disarmed} > Use mri_vol2vol, eg, > mri_vol2vol --mov filtered_func_data.nii.gz --reg > partial-to-struct.lta –o ffd-struct.nii.gz --fstarg > > On 6/18/2020 10:43 AM, Mason Wells wrote: >> >> External Email - Use Caution >> >> Hi Doug, >> >> I have just one final question RE this registration pipeline. So far >> it’s worked great for 9/10 PPTs, so thanks. I assume there isn’t much >> I can do about the 1/10 participant? However, the original plan was >> to get this transformation matrix (partial-to-struct.lta) and use it >> in mri_vol2surf. However, if I want to just apply the final >> transformation to the filtered_func.nii.gz file, can I just simple >> run the following command with –o to apply the transformation >> directly to the filtered_func.nii.gz inside the bbregister command? >> Or will I have to take the partial-to-struct.lta and apply it in >> something like applyxfm? >> >> bbregister --mov filtered_func_data.nii.gz --init-reg >> partial-to-struct.init.lta --reg partial-to-struct.lta --t2 –o >> >> Thanks, >> >> Mason >> >> *Mason T Wells, MSc* >> >> *PhD student* >> >> School of Optometry and Vision Sciences >> >> & Cardiff University Brain Research >> >> Imaging Centre (CUBRIC), School of Psychology >> >> Cardiff University >> >> Cardiff >> >> CF24 4HQ >> >> UK >> >> */Email/*: WellsMT1(a)cardiff.ac.uk <mailto:WellsMT1@cardiff.ac.uk> >> >> */Tel/*: 02920 879628 >> >> */Web/*: Cardiff University webpage >> <https://www.cardiff.ac.uk/people/research-students/view/974214-> >> >> >> >> *Mason T Wells, MSc* >> >> *Myfyriwr PhD* >> >> Yr Ysgol Optometreg a Gwyddorau’r Golwg >> >> & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), >> Yr Ysgol Seicoleg >> >> Prifysgol Caerdydd >> >> Heol Maindy >> >> Caerdydd >> >> CF24 4HQ >> >> DU >> >> */E-bost/*: WellsMT1(a)caerdydd.ac.uk <mailto:WellsMT1@caerdydd.ac.uk> >> >> */Ffôn/*: 02920 879628 >> >> *From: *"Douglas N. Greve" <dgreve(a)mgh.harvard.edu> >> <mailto:dgreve@mgh.harvard.edu> >> *Date: *Wednesday, 3 June 2020 at 22:09 >> *To: *Mason Wells <WellsMT1(a)cardiff.ac.uk> >> <mailto:WellsMT1@cardiff.ac.uk>, Freesurfer support list >> <freesurfer(a)nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Subject: *Re: [Freesurfer] Bbregister misalignment {Disarmed} >> >> There is nothing in bbr that will directly do this, but you can hack it. >> >> Once you run flirt and get the .mat file, run >> tkregister2 --mov partial.nii.gz --targ whole.nii.gz --fslmat >> flirt.mat --reg partial-to-whole.dat --ltaout partial-to-whole.lta >> This will bring up a window where you can verify that the >> registration looks ok. Hit the "Save Reg" button. You don't have to >> do this everytime, but the first time it is a good idea. Once you >> have confidence, you can run tkregister2 with --noedit, and it will >> just return creating the .dat and .lta files >> >> Run bbregister with the whole brain epi to get an LTA file (eg, >> whole-to-struct.lta) >> >> Now combine them with >> mri_concatenate_lta -subject subject partial-to-whole.lta >> whole-to-struct.lta partial-to-struct.init.lta >> >> Verify that the reg looks ok wtih >> tkregister2 --mov partial.nii.gz --reg junk.dat --lta >> partial-to-struct.init.lta >> >> Then run bbr like >> bbregister --mov partial.nii.gz --init-reg >> partial-to-struct.init.lta -reg partial-to-struct.lta --t2 >> >> >> On 6/3/2020 1:25 PM, Mason Wells wrote: >> >> * External Email - Use Caution * >> >> Just another point, Doug. The whole brain to partial epi >> registers fine in Feat. The alignment looks good. So, I guess I >> have two questions. Is there something in bbregister that can get >> the alignment of the partial and whole brain epi to match (as in >> Feat), and in the case where a whole brain isn’t acquired, what >> command/flags should be used in order to get the partial epi to >> align with the anatomical? >> >> Cheers, >> >> Mason >> >> *Mason T Wells, MSc* >> >> *PhD student* >> >> School of Optometry and Vision Sciences >> >> & Cardiff University Brain Research >> >> Imaging Centre (CUBRIC), School of Psychology >> >> Cardiff University >> >> Cardiff >> >> CF24 4HQ >> >> UK >> >> */Email/*: WellsMT1(a)cardiff.ac.uk <mailto:WellsMT1@cardiff.ac.uk> >> >> */Tel/*: 02920 879628 >> >> */Web/*: Cardiff University webpage >> <https://www.cardiff.ac.uk/people/research-students/view/974214-> >> >> >> >> *Mason T Wells, MSc* >> >> *Myfyriwr PhD* >> >> Yr Ysgol Optometreg a Gwyddorau’r Golwg >> >> & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd >> (CUBRIC), Yr Ysgol Seicoleg >> >> Prifysgol Caerdydd >> >> Heol Maindy >> >> Caerdydd >> >> CF24 4HQ >> >> DU >> >> */E-bost/*: WellsMT1(a)caerdydd.ac.uk <mailto:WellsMT1@caerdydd.ac.uk> >> >> */Ffôn/*: 02920 879628 >> >> *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of >> Mason Wells <WellsMT1(a)cardiff.ac.uk> <mailto:WellsMT1@cardiff.ac.uk> >> *Reply to: *Freesurfer support list >> <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Date: *Wednesday, 3 June 2020 at 18:20 >> *To: *"Douglas N. Greve" <dgreve(a)mgh.harvard.edu> >> <mailto:dgreve@mgh.harvard.edu>, Freesurfer support list >> <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Subject: *Re: [Freesurfer] Bbregister misalignment {Disarmed} >> >> * External Email - Use Caution * >> >> Thanks, Doug. >> >> How would I go about getting the partial EPI to register with the >> T1? You can see in my previous emails, I just haven’t been able >> to get this to work. I have been using the –feat flag, can I >> still use this? >> >> Any help on this would be great. >> >> Sorry, I am just unsure with the possible flag combinations. >> >> *Mason T Wells, MSc* >> >> *PhD student* >> >> School of Optometry and Vision Sciences >> >> & Cardiff University Brain Research >> >> Imaging Centre (CUBRIC), School of Psychology >> >> Cardiff University >> >> Cardiff >> >> CF24 4HQ >> >> UK >> >> */Email/*: WellsMT1(a)cardiff.ac.uk <mailto:WellsMT1@cardiff.ac.uk> >> >> */Tel/*: 02920 879628 >> >> */Web/*: Cardiff University webpage >> <https://www.cardiff.ac.uk/people/research-students/view/974214-> >> >> >> >> *Mason T Wells, MSc* >> >> *Myfyriwr PhD* >> >> Yr Ysgol Optometreg a Gwyddorau’r Golwg >> >> & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd >> (CUBRIC), Yr Ysgol Seicoleg >> >> Prifysgol Caerdydd >> >> Heol Maindy >> >> Caerdydd >> >> CF24 4HQ >> >> DU >> >> */E-bost/*: WellsMT1(a)caerdydd.ac.uk <mailto:WellsMT1@caerdydd.ac.uk> >> >> */Ffôn/*: 02920 879628 >> >> *From: *"Douglas N. Greve" <dgreve(a)mgh.harvard.edu> >> <mailto:dgreve@mgh.harvard.edu> >> *Date: *Wednesday, 3 June 2020 at 18:11 >> *To: *Mason Wells <WellsMT1(a)cardiff.ac.uk> >> <mailto:WellsMT1@cardiff.ac.uk>, Freesurfer support list >> <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Subject: *Re: [Freesurfer] Bbregister misalignment {Disarmed} >> >> yes, sometimes it will work ok and sometimes it won't. Partial >> FoV registration to a whole brain can be finicky. But if it >> works, then nothing wrong with it. >> >> On 6/3/2020 12:49 PM, Mason Wells wrote: >> >> * External Email - Use Caution * >> >> I am really not sure, sorry. This is a secondary data set >> that I am using, I didn’t collect these data. For a number of >> the PPTS, there is no whole brain volume. Which is why I >> wondered if I could get a good registration without it. For >> 3/10 it worked fine as I was just running: >> >> bbregister --s PPT_001 --feat >> /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_functional.feat/ >> --init-coreg >> >> As you can see, the whole brain and T1 registered well with >> the second command you sent. Is there a way I can do >> something similar with just the partial FOV epi? >> >> Thanks for your help with this. >> >> *Mason T Wells, MSc* >> >> *PhD student* >> >> School of Optometry and Vision Sciences >> >> & Cardiff University Brain Research >> >> Imaging Centre (CUBRIC), School of Psychology >> >> Cardiff University >> >> Cardiff >> >> CF24 4HQ >> >> UK >> >> */Email/*: WellsMT1(a)cardiff.ac.uk <mailto:WellsMT1@cardiff.ac.uk> >> >> */Tel/*: 02920 879628 >> >> */Web/*: Cardiff University webpage >> <https://www.cardiff.ac.uk/people/research-students/view/974214-> >> >> >> >> *Mason T Wells, MSc* >> >> *Myfyriwr PhD* >> >> Yr Ysgol Optometreg a Gwyddorau’r Golwg >> >> & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd >> (CUBRIC), Yr Ysgol Seicoleg >> >> Prifysgol Caerdydd >> >> Heol Maindy >> >> Caerdydd >> >> CF24 4HQ >> >> DU >> >> */E-bost/*: WellsMT1(a)caerdydd.ac.uk >> <mailto:WellsMT1@caerdydd.ac.uk> >> >> */Ffôn/*: 02920 879628 >> >> *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of >> "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> >> <mailto:dgreve@mgh.harvard.edu> >> *Reply to: *Freesurfer support list >> <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Date: *Wednesday, 3 June 2020 at 17:45 >> *To: *"freesurfer(a)nmr.mgh.harvard.edu" >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Subject: *Re: [Freesurfer] Bbregister misalignment {Disarmed} >> >> You can ignore that warning. The source of the problem is >> that the whole-brain and the partial FoV are not in >> alignment. The idea here is that you acquire the whole head >> and the partial fov in the same scanning session so that they >> are more-or-less in alignment. When you register the whole >> brain to the structural, you can then get the partial fov to >> structural by concatenating the registrations. So, why is >> your whole brain out of alignment with the partial fov? >> >> On 6/3/2020 12:31 PM, Mason Wells wrote: >> >> * External Email - Use Caution * >> >> Hi Doug, >> >> Do you mean to raw partial epi and the whole brain? If >> so, I have ran: >> >> tkregisterfv --mov >> /home/c1749990/data/PhD/Data/PMA_retinoScans/PPT_002/run1.nii.gz >> --targ >> /home//c1749990/data/PhD/Data/PMA_retinoScans/PPT_002/WholeEPI.nii.gz >> --regheader --reg partial-to-full.lta >> >> but the once Freeview opens, the terminal states: >> >> Warning: Transformation can only apply to volumes for >> now. If your data includes ROI/Surface/Way Points, please >> do not use this feature yet. >> >> INFO: LTA input is not RAS to RAS...converting... >> >> Also, in the freeview window, the whole brain and the raw >> epi are very misaligned as I click between displaying the >> two volumes in Freeview (attached). I should also add, of >> the 10 I have ran I did not use the whole brain –int flag >> as it appeared to make the registration a lot worse than >> just running: >> >> bbregister --s PPT_002 --feat >> /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_002/run1.feat/ >> --init-coreg >> >> Should I still try and register the whole epi to the T1 >> (structural)? >> >> *Mason T Wells, MSc* >> >> *PhD student* >> >> School of Optometry and Vision Sciences >> >> & Cardiff University Brain Research >> >> Imaging Centre (CUBRIC), School of Psychology >> >> Cardiff University >> >> Cardiff >> >> CF24 4HQ >> >> UK >> >> */Email/*: WellsMT1(a)cardiff.ac.uk >> <mailto:WellsMT1@cardiff.ac.uk> >> >> */Tel/*: 02920 879628 >> >> */Web/*: Cardiff University webpage >> <https://www.cardiff.ac.uk/people/research-students/view/974214-> >> >> >> >> *Mason T Wells, MSc* >> >> *Myfyriwr PhD* >> >> Yr Ysgol Optometreg a Gwyddorau’r Golwg >> >> & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd >> (CUBRIC), Yr Ysgol Seicoleg >> >> Prifysgol Caerdydd >> >> Heol Maindy >> >> Caerdydd >> >> CF24 4HQ >> >> DU >> >> */E-bost/*: WellsMT1(a)caerdydd.ac.uk >> <mailto:WellsMT1@caerdydd.ac.uk> >> >> */Ffôn/*: 02920 879628 >> >> *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf >> of "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> >> <mailto:dgreve@mgh.harvard.edu> >> *Reply to: *Freesurfer support list >> <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Date: *Wednesday, 3 June 2020 at 17:14 >> *To: *"freesurfer(a)nmr.mgh.harvard.edu" >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Subject: *Re: [Freesurfer] Bbregister misalignment >> {Disarmed} >> >> >> A couple of things to try: >> >> First, make sure that the whole head and the partial FoV >> EPIs are in register without doing any registration >> tkregisterfv --mov partialfovepi.nii.gz --targ >> wholeepi.nii.gz --regheader --reg partial-to-full.lta >> >> Next, register the whole head EPI to the structural >> bbregister --mov wholeepi.nii.gz --s subject --t2 --reg >> whole-to-struct.lta >> View the result and make sure that it is in register >> >> Let me know how that goes >> >> >> >> >> >> On 6/3/2020 11:33 AM, Mason Wells wrote: >> >> * External Email - Use Caution * >> >> Sorry for yet another email on this, but 3/10 PPTs >> ended up with a good reg from bbregister, all using >> the same command. The issue is always when the epi >> orientation is like the attached. Have you any idea >> what to do? It's almost like bbregister can't >> orientate the brain so the epi is in the plane as the >> white matter. An epi slice is diagonal and the >> structural slice is horizontal, and this is where the >> issue is. >> >> Cheers, >> >> Mason >> >> *Mason T Wells, MSc* >> >> *PhD student* >> >> School of Optometry and Vision Sciences >> >> & Cardiff University Brain Research >> >> Imaging Centre (CUBRIC), School of Psychology >> >> Cardiff University >> >> Cardiff >> >> CF24 4HQ >> >> UK >> >> */Email/*: WellsMT1(a)cardiff.ac.uk >> <mailto:WellsMT1@cardiff.ac.uk> >> >> */Tel/*: 02920 879628 >> >> */Web/*: Cardiff University webpage >> <https://www.cardiff.ac.uk/people/research-students/view/974214-> >> >> >> >> *Mason T Wells, MSc* >> >> *Myfyriwr PhD* >> >> Yr Ysgol Optometreg a Gwyddorau’r Golwg >> >> & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol >> Caerdydd (CUBRIC), Yr Ysgol Seicoleg >> >> Prifysgol Caerdydd >> >> Heol Maindy >> >> Caerdydd >> >> CF24 4HQ >> >> DU >> >> */E-bost/*: WellsMT1(a)caerdydd.ac.uk >> <mailto:WellsMT1@caerdydd.ac.uk> >> >> */Ffôn/*: 02920 879628 >> >> *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on >> behalf of Mason Wells <WellsMT1(a)cardiff.ac.uk> >> <mailto:WellsMT1@cardiff.ac.uk> >> *Reply to: *Freesurfer support list >> <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Date: *Wednesday, 3 June 2020 at 14:05 >> *To: *Freesurfer support list >> <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Subject: *Re: [Freesurfer] Bbregister misalignment >> {Disarmed} >> >> * External Email - Use Caution * >> >> Hi Doug, >> >> Thanks for this. However, I can’t seem to access the ftp: >> >> c1749990@l017:~/data/freesurfer/subjects$ ftp >> surfer.nmr.mgh.harvard.edu >> >> bash: ftp: command not found... >> >> Is there another way to do this? >> >> Cheers, >> >> Mason >> >> *Mason T Wells, MSc* >> >> *PhD student* >> >> School of Optometry and Vision Sciences >> >> & Cardiff University Brain Research >> >> Imaging Centre (CUBRIC), School of Psychology >> >> Cardiff University >> >> Cardiff >> >> CF24 4HQ >> >> UK >> >> */Email/*: WellsMT1(a)cardiff.ac.uk >> <mailto:WellsMT1@cardiff.ac.uk> >> >> */Tel/*: 02920 879628 >> >> */Web/*: Cardiff University webpage >> <https://www.cardiff.ac.uk/people/research-students/view/974214-> >> >> >> >> *Mason T Wells, MSc* >> >> *Myfyriwr PhD* >> >> Yr Ysgol Optometreg a Gwyddorau’r Golwg >> >> & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol >> Caerdydd (CUBRIC), Yr Ysgol Seicoleg >> >> Prifysgol Caerdydd >> >> Heol Maindy >> >> Caerdydd >> >> CF24 4HQ >> >> DU >> >> */E-bost/*: WellsMT1(a)caerdydd.ac.uk >> <mailto:WellsMT1@caerdydd.ac.uk> >> >> */Ffôn/*: 02920 879628 >> >> *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on >> behalf of "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> >> <mailto:dgreve@mgh.harvard.edu> >> *Reply to: *Freesurfer support list >> <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Date: *Tuesday, 2 June 2020 at 18:39 >> *To: *"freesurfer(a)nmr.mgh.harvard.edu" >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Subject: *Re: [Freesurfer] Bbregister misalignment >> {Disarmed} >> >> If you upload the data, I'll take a look. Upload both >> the structural and the fMRI. See instructions below >> >> From the linux command line, >> Create the file you want to upload, eg, >> cd $SUBJECTS_DIR >> tar cvfz subject.tar.gz ./subject >> Now log into our anonymous FTP site: >> ftp surfer.nmr.mgh.harvard.edu >> It will ask you for a user name: use "anonymous" (no >> quotes) >> It will ask you for a password: use "anonymous" (no >> quotes) >> cd transfer/incoming >> binary >> put subject.tar.gz >> Send an email that the file has been and the name of >> the file. >> >> >> >> >> >> >> >> >> On 6/2/2020 9:14 AM, Mason Wells wrote: >> >> * External Email - Use Caution * >> >> Just a follow up here. I tried the command below >> on a machine with v.6, and the flag was >> recognised, but the registration was still off. >> No change to the output with the flag included. >> >> *Mason T Wells, MSc* >> >> *PhD student* >> >> School of Optometry and Vision Sciences >> >> & Cardiff University Brain Research >> >> Imaging Centre (CUBRIC), School of Psychology >> >> Cardiff University >> >> Cardiff >> >> CF24 4HQ >> >> UK >> >> */Email/*: WellsMT1(a)cardiff.ac.uk >> <mailto:WellsMT1@cardiff.ac.uk> >> >> */Tel/*: 02920 879628 >> >> */Web/*: Cardiff University webpage >> <https://www.cardiff.ac.uk/people/research-students/view/974214-> >> >> >> >> *Mason T Wells, MSc* >> >> *Myfyriwr PhD* >> >> Yr Ysgol Optometreg a Gwyddorau’r Golwg >> >> & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol >> Caerdydd (CUBRIC), Yr Ysgol Seicoleg >> >> Prifysgol Caerdydd >> >> Heol Maindy >> >> Caerdydd >> >> CF24 4HQ >> >> DU >> >> */E-bost/*: WellsMT1(a)caerdydd.ac.uk >> <mailto:WellsMT1@caerdydd.ac.uk> >> >> */Ffôn/*: 02920 879628 >> >> *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >> on behalf of Mason Wells <WellsMT1(a)cardiff.ac.uk> >> <mailto:WellsMT1@cardiff.ac.uk> >> *Reply to: *Freesurfer support list >> <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Date: *Tuesday, 2 June 2020 at 14:06 >> *To: *Freesurfer support list >> <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Subject: *Re: [Freesurfer] Bbregister >> misalignment {Disarmed} >> >> * External Email - Use Caution * >> >> Hi Doug, >> >> I have FS v6.0 and tried the following command: >> >> ERROR: Flag --init-coreg unrecognized. >> >> --s PPT_001 --feat >> /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_functional.feat/ >> --int >> /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/WholeEPI.nii.gz >> --init-header --init-coreg >> >> Still get the error. Is this correct use of the >> flags? >> >> *Mason T Wells, MSc* >> >> *PhD student* >> >> School of Optometry and Vision Sciences >> >> & Cardiff University Brain Research >> >> Imaging Centre (CUBRIC), School of Psychology >> >> Cardiff University >> >> Cardiff >> >> CF24 4HQ >> >> UK >> >> */Email/*: WellsMT1(a)cardiff.ac.uk >> <mailto:WellsMT1@cardiff.ac.uk> >> >> */Tel/*: 02920 879628 >> >> */Web/*: Cardiff University webpage >> <https://www.cardiff.ac.uk/people/research-students/view/974214-> >> >> >> >> *Mason T Wells, MSc* >> >> *Myfyriwr PhD* >> >> Yr Ysgol Optometreg a Gwyddorau’r Golwg >> >> & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol >> Caerdydd (CUBRIC), Yr Ysgol Seicoleg >> >> Prifysgol Caerdydd >> >> Heol Maindy >> >> Caerdydd >> >> CF24 4HQ >> >> DU >> >> */E-bost/*: WellsMT1(a)caerdydd.ac.uk >> <mailto:WellsMT1@caerdydd.ac.uk> >> >> */Ffôn/*: 02920 879628 >> >> *From: *<freesurfer-bounces(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >> on behalf of "Douglas N. Greve" >> <dgreve(a)mgh.harvard.edu> >> <mailto:dgreve@mgh.harvard.edu> >> *Reply to: *Freesurfer support list >> <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Date: *Tuesday, 2 June 2020 at 13:48 >> *To: *"freesurfer(a)nmr.mgh.harvard.edu" >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Subject: *Re: [Freesurfer] Bbregister >> misalignment {Disarmed} >> >> Right now, I'm just guessing what the problem is >> (I'm speculating that it is FSL FLIRT). You could >> download just the new bbregister and mri_coreg to >> your VM and see if it works. >> >> >> >> >> >> >> >> >> >> >> On 6/2/2020 6:40 AM, Mason Wells wrote: >> >> * External Email - Use Caution * >> >> I am using version 5.3, this is the version >> on the virtual machine I am working from. I >> can ask about an updated version, but is >> there a way to fix this on v5.3 in the meantime? >> >> *Mason T Wells, MSc* >> >> *PhD student* >> >> School of Optometry and Vision Sciences >> >> & Cardiff University Brain Research >> >> Imaging Centre (CUBRIC), School of Psychology >> >> Cardiff University >> >> Cardiff >> >> CF24 4HQ >> >> UK >> >> */Email/*: WellsMT1(a)cardiff.ac.uk >> <mailto:WellsMT1@cardiff.ac.uk> >> >> */Tel/*: 02920 879628 >> >> */Web/*: Cardiff University webpage >> <https://www.cardiff.ac.uk/people/research-students/view/974214-> >> >> >> >> *Mason T Wells, MSc* >> >> *Myfyriwr PhD* >> >> Yr Ysgol Optometreg a Gwyddorau’r Golwg >> >> & Canolfan Ymchwil Delweddu’r Ymennydd >> Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg >> >> Prifysgol Caerdydd >> >> Heol Maindy >> >> Caerdydd >> >> CF24 4HQ >> >> DU >> >> */E-bost/*: WellsMT1(a)caerdydd.ac.uk >> <mailto:WellsMT1@caerdydd.ac.uk> >> >> */Ffôn/*: 02920 879628 >> >> *From: >> *<freesurfer-bounces(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >> on behalf of "Douglas N. Greve" >> <dgreve(a)mgh.harvard.edu> >> <mailto:dgreve@mgh.harvard.edu> >> *Reply to: *Freesurfer support list >> <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Date: *Monday, 1 June 2020 at 18:02 >> *To: *"freesurfer(a)nmr.mgh.harvard.edu" >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Subject: *Re: [Freesurfer] Bbregister >> misalignment {Disarmed} >> >> What version of FS are you running? That flag >> was introduced with v6 >> >> On 6/1/2020 12:57 PM, Mason Wells wrote: >> >> * External Email - Use Caution * >> >> Hi Doug, >> >> That flag isn’t recognised in the >> terminal? Have I placed the flag in the >> wrong place? I tried it between the –feat >> and the directory, same outcome. >> >> bbregister --s PPT_001 --feat >> /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_functional.feat/ >> --int >> /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/WholeEPI.nii.gz >> --init-header --init-coreg >> >> ERROR: Flag --init-coreg unrecognized. >> >> --s PPT_001 --feat >> /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_ >> >> *Mason T Wells, MSc* >> >> *PhD student* >> >> School of Optometry and Vision Sciences >> >> & Cardiff University Brain Research >> >> Imaging Centre (CUBRIC), School of Psychology >> >> Cardiff University >> >> Cardiff >> >> CF24 4HQ >> >> UK >> >> */Email/*: WellsMT1(a)cardiff.ac.uk >> <mailto:WellsMT1@cardiff.ac.uk> >> >> */Tel/*: 02920 879628 >> >> */Web/*: Cardiff University webpage >> <https://www.cardiff.ac.uk/people/research-students/view/974214-> >> >> >> >> *Mason T Wells, MSc* >> >> *Myfyriwr PhD* >> >> Yr Ysgol Optometreg a Gwyddorau’r Golwg >> >> & Canolfan Ymchwil Delweddu’r Ymennydd >> Prifysgol Caerdydd (CUBRIC), Yr Ysgol >> Seicoleg >> >> Prifysgol Caerdydd >> >> Heol Maindy >> >> Caerdydd >> >> CF24 4HQ >> >> DU >> >> */E-bost/*: WellsMT1(a)caerdydd.ac.uk >> <mailto:WellsMT1@caerdydd.ac.uk> >> >> */Ffôn/*: 02920 879628 >> >> *From: >> *<freesurfer-bounces(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >> on behalf of "Douglas N. Greve" >> <dgreve(a)mgh.harvard.edu> >> <mailto:dgreve@mgh.harvard.edu> >> *Reply to: *Freesurfer support list >> <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Date: *Monday, 1 June 2020 at 17:38 >> *To: *"freesurfer(a)nmr.mgh.harvard.edu" >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Subject: *Re: [Freesurfer] Bbregister >> misalignment >> >> Sorry for missing your first email. Can >> you try adding --init-coreg to your first >> bbregister command? Make sure to add it >> AFTER --feat >> >> On 6/1/2020 12:06 PM, Mason Wells wrote: >> >> * External Email - Use Caution * >> >> Hi Experts, >> >> I posted earlier, but I believe my >> message has not been posted due to >> the size of attachments so I’ve >> removed them. >> >> I am using bbregister to align >> functional data to anatomical space. >> I have been using the bbregister >> command with a combination of >> different flags. However, there >> appears to be varying levels of poor >> registration. >> >> The first command I used included >> flags for a whole brain ref image and >> the --init-header flag. This leads to >> a misalignment. >> >> bbregister --s PPT_1x --feat >> /Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat/ >> --int >> Data/PMA_retinoScans/PPT_1x/WholeEPI.nii.gz >> --init-header >> >> I then removed the –int (whole brain >> reg image) flag. Again the >> registration is massively misaligned. >> >> bbregister --s PPT_1x --feat >> /Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat >> --init-header >> >> I then removed the –init-header flag. >> Again poor registration. >> >> Then I removed both flags. This was >> the best registration, but even this >> still looks a little bit off to me. >> You can see that around the occipital >> lobe (reg3 attached), there white >> matter isn't aligned very well. >> >> bbregister --s PPT_1x --feat >> /Data/PPT_1x/run1_pre_processed_functional.feat/ >> >> Can anyone give me any advice on >> this? I really am unsure as to which >> why these flags failed to aid >> registration. I have 3 other >> participants from a different dataset >> for which the bbregister pointing to >> the feat directory *and *the >> –init-header flag worked perfectly. >> Have I missed an important step that >> could explain why no combination >> seems to register the data correctly? >> >> Any advice would be great. >> >> Thanks in advance, >> >> Mason >> >> *Mason T Wells, MSc* >> >> *PhD student* >> >> School of Optometry and Vision Sciences >> >> & Cardiff University Brain Research >> >> Imaging Centre (CUBRIC), School of >> Psychology >> >> Cardiff University >> >> Cardiff >> >> CF24 4HQ >> >> UK >> >> */Email/*: WellsMT1(a)cardiff.ac.uk >> <mailto:WellsMT1@cardiff.ac.uk> >> >> */Tel/*: 02920 879628 >> >> */Web/*: Cardiff University webpage >> <https://www.cardiff.ac.uk/people/research-students/view/974214-> >> >> >> >> *Mason T Wells, MSc* >> >> *Myfyriwr PhD* >> >> Yr Ysgol Optometreg a Gwyddorau’r Golwg >> >> & Canolfan Ymchwil Delweddu’r >> Ymennydd Prifysgol Caerdydd (CUBRIC), >> Yr Ysgol Seicoleg >> >> Prifysgol Caerdydd >> >> Heol Maindy >> >> Caerdydd >> >> CF24 4HQ >> >> DU >> >> */E-bost/*: WellsMT1(a)caerdydd.ac.uk >> <mailto:WellsMT1@caerdydd.ac.uk> >> >> */Ffôn/*: 02920 879628 >> >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> *MailScanner has detected a possible >> fraud attempt from >> "eur03.safelinks.protection.outlook.com" >> claiming to be* >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.…> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> *MailScanner has detected a possible >> fraud attempt from >> "eur03.safelinks.protection.outlook.com" >> claiming to be* >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.…> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> *MailScanner has detected a possible fraud >> attempt from >> "eur03.safelinks.protection.outlook.com" >> claiming to be* >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.…> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> *MailScanner has detected a possible fraud >> attempt from >> "eur03.safelinks.protection.outlook.com" claiming >> to be* >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.…> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> *MailScanner has detected a possible fraud attempt >> from "eur03.safelinks.protection.outlook.com" >> claiming to be* >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.…> >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >> *MailScanner has detected a possible fraud attempt from >> "eur03.safelinks.protection.outlook.com" claiming to be* >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.…> >> >> >> >> >> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error >> and the e-mail >> contains patient information, please contact the Partners >> Compliance HelpLine at >> http://www.partners.org/complianceline >> <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.partne…> >> . If the e-mail was sent to you in error >> but does not contain patient information, please contact the >> sender and properly >> dispose of the e-mail. >> >> >> >

1 0

How to get access to the coordinate data of specified area
by Chen Yu 18 Jun '20

18 Jun '20

External Email - Use Caution Hello, I found FreeSurfer can segment brain areas automatically these days, and it really meets my requirements. therefore, this tool is really useful for me! But this process is only a part of my work, and I notice FreeSurfer isn't designed for third-party usage. Otherwise, I still want to enroll this function in my project. Could you please tell me if I can import Freesurfer to my project and how. Or how to get the result coordinate data of brain parcellation so that I can locate the position of a specific area(just like 'aseg.mgz' file do)? Looking forward to hearing from you! sincerely Fritz.

3 2

Visualization of FreeSurfer overlays in the HCP format
by Katsumi, Yuta 18 Jun '20

18 Jun '20

Dear FreeSurfer community, I would like to be able to display OVERLAY files generated in FreeSurfer on a surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The HCP team states in their documentation (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersF…) that any surfaces to be converted to fs_LR need to be in .gii first, but I know mris_convert doesn’t take overlay files as input. It would be great if you could please let me know how I might be able to achieve this task. Thanks, Yuta

1 0

Re: [Freesurfer] VM ubuntu developer password
by fsbuild 18 Jun '20

18 Jun '20

External Email - Use Caution Ok Cyrus - I have just sent it to your email. - R. Sarosh, Cyrus June 18, 2020 at 16:02         External Email - Use Caution         I have also just ran into this issue. Can someone send me the password as well? Thansk, Cyrus Cyrus Sarosh Research Area Specialist Intermediate Department of Radiology Functional Neuroimaging, Cognitive and Mobility Laboratory Domino’s Farms  Lobby B Suite 1200 24 Frank Lloyd Wright Dr  PO BOX 362 Ann Arbor, MI 48106 t: 734-998-4790 f: 734-998-8403 From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of FAIRS Amie <amie.FAIRS(a)univ-amu.fr> Sent: Thursday, June 18, 2020 1:43 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] VM ubuntu developer password   External Email - Use Caution         External Email - Use Caution         Hello everyone,   I have been sent the VM ubuntu password. But in case this is useful for others – at least on my laptop the ubuntu distribution is using a US/international QWERTY keyboard. My laptop has an AZERTY keyboard (French) and so I had some problems with the password being rejected. In case future VM users encounter errors entering the password, you may need to switch keyboard layout..   Thank you to the people who sent me the password so speedily!   Best,   Amie   ------------------   Dr. Amie Fairs Post-doctorant Aix-Marseille Université Laboratoire Parole et Langage (LPL) | CNRS UMR 7309 | 5 Avenue Pasteur | 13100 Aix-en-Provence Email : amie.fairs(a)univ-amu.fr   While I may send this email outside of typical working hours, I have no expectation to receive an email outside of your typical hours..   From: fsbuild <fsbuild(a)contbay.com> Sent: 18 June 2020 19:24 To: freesurfer(a)nmr.mgh.harvard.edu Cc: FAIRS Amie <amie.FAIRS(a)univ-amu.fr> Subject: Re: [Freesurfer] VM ubuntu developer password   Hello Amie,   I have just sent the password to your private email.   - R.   ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer FAIRS Amie June 18, 2020 at 13:43         External Email - Use Caution         Hello everyone,   I have been sent the VM ubuntu password. But in case this is useful for others – at least on my laptop the ubuntu distribution is using a US/international QWERTY keyboard. My laptop has an AZERTY keyboard (French) and so I had some problems with the password being rejected. In case future VM users encounter errors entering the password, you may need to switch keyboard layout.   Thank you to the people who sent me the password so speedily!   Best,   Amie   ------------------   Dr. Amie Fairs Post-doctorant Aix-Marseille Université Laboratoire Parole et Langage (LPL) | CNRS UMR 7309 | 5 Avenue Pasteur | 13100 Aix-en-Provence Email : amie.fairs(a)univ-amu.fr   While I may send this email outside of typical working hours, I have no expectation to receive an email outside of your typical hours.   From: fsbuild <fsbuild(a)contbay.com> Sent: 18 June 2020 19:24 To: freesurfer(a)nmr.mgh.harvard.edu Cc: FAIRS Amie <amie.FAIRS(a)univ-amu.fr> Subject: Re: [Freesurfer] VM ubuntu developer password   Hello Amie,   I have just sent the password to your private email.   - R.   _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer fsbuild June 18, 2020 at 13:24         External Email - Use Caution        Hello Amie, I have just sent the password to your private email. - R. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Re: [Freesurfer] VM ubuntu developer password
by fsbuild 18 Jun '20

18 Jun '20

External Email - Use Caution Hello Amie, I have just sent the password to your private email. - R. On Jun 18, 2020, at 08:57, FAIRS Amie <amie.FAIRS(a)univ-amu.fr> wrote:        External Email - Use Caution        Dear Freesurfer mailing list, I have just downloaded the virtual machine + ubuntu package, as outlined on the website when running a VM in windows. However, ubuntu is asking for a developer password to open within the VM. I see on the help page (on the website) that the log in ID could be in the README doc, but I can’t actually get the VM open to get there. Does anyone know the password so I can set up the VM and get started with freesurfer? Thanks so much in advance! Best, Amie ------------------  Dr. Amie FairsPost-doctorantAix-Marseille UniversitéLaboratoire Parole et Langage (LPL) | CNRS UMR 7309 | 5 Avenue Pasteur | 13100 Aix-en-ProvenceEmail : amie.fairs@univ-amu.fr While I may send this email outside of typical working hours, I have no expectation to receive an email outside of your typical hours. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

3 2

recon-all for macaque brain
by Minqing Jiang 18 Jun '20

18 Jun '20

External Email - Use Caution Hi there, I'm running freesurfer to analyze macaque brain. Since the monkey brain is much smaller than human brain. We use 0.5*05* 05mm to scan the monkey brain. Is there anyway I can avoid downsampling the scan resolution to 1*1*1mm by recon-all? Thank you so much. Please allow me to apologize if I ask a naive question. bests, Minqing

2 1

Bbregister misalignment
by Mason Wells 18 Jun '20

18 Jun '20

External Email - Use Caution Hi Experts, I posted earlier, but I believe my message has not been posted due to the size of attachments so I’ve removed them. I am using bbregister to align functional data to anatomical space. I have been using the bbregister command with a combination of different flags. However, there appears to be varying levels of poor registration. The first command I used included flags for a whole brain ref image and the --init-header flag. This leads to a misalignment. bbregister --s PPT_1x --feat /Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat/ --int Data/PMA_retinoScans/PPT_1x/WholeEPI.nii.gz --init-header I then removed the –int (whole brain reg image) flag. Again the registration is massively misaligned. bbregister --s PPT_1x --feat /Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat --init-header I then removed the –init-header flag. Again poor registration. Then I removed both flags. This was the best registration, but even this still looks a little bit off to me. You can see that around the occipital lobe (reg3 attached), there white matter isn't aligned very well. bbregister --s PPT_1x --feat /Data/PPT_1x/run1_pre_processed_functional.feat/ Can anyone give me any advice on this? I really am unsure as to which why these flags failed to aid registration. I have 3 other participants from a different dataset for which the bbregister pointing to the feat directory and the –init-header flag worked perfectly. Have I missed an important step that could explain why no combination seems to register the data correctly? Any advice would be great. Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

2 25

Freeview - Load custom overlay from terminal
by Loucao, Ricardo 18 Jun '20

18 Jun '20

External Email - Use Caution Dear FS experts, I’m trying to load a surface with a custom overlay directly from the terminal using the sub-option “overlay_custom” but it returns “Unrecognized sub-option flag ‘overlay_custom’”. I checked the source code on GitHub and found the flag to be present and implemented. I also built the freeview app from the GitHub (as it could be that my version did not have that sub-option) but I got the same return message. Upon inspecting the code further, I figured the way this flag works is via quadruplets of the form “val, r, g, b”. However, I also noticed that this return message comes when the overlay_custom sub-option is empty (freeview/MainWindow.cpp: line 3484). It seems to me like I might be using the flag improperly. Here’s an example of how I am using it: “:overlay_custom=0.85,255,0,0,0.875,0,255,255,0.90,0,0,255” Do you have any hints for me on how to deal with this? Thank you very much in advance! Best regards, Ricardo ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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VM ubuntu developer password
by FAIRS Amie 18 Jun '20

18 Jun '20

External Email - Use Caution Dear Freesurfer mailing list, I have just downloaded the virtual machine + ubuntu package, as outlined on the website when running a VM in windows. However, ubuntu is asking for a developer password to open within the VM. I see on the help page (on the website) that the log in ID could be in the README doc, but I can't actually get the VM open to get there. Does anyone know the password so I can set up the VM and get started with freesurfer? Thanks so much in advance! Best, Amie ------------------ Dr. Amie Fairs Post-doctorant Aix-Marseille Université Laboratoire Parole et Langage (LPL) | CNRS UMR 7309 | 5 Avenue Pasteur | 13100 Aix-en-Provence Email : amie.fairs(a)univ-amu.fr<mailto:amie.fairs@univ-amu.fr> While I may send this email outside of typical working hours, I have no expectation to receive an email outside of your typical hours.

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Correcting recon-all output (missing parts in pial surface)
by Michael 17 Jun '20

17 Jun '20

External Email - Use Caution Hello, I ran recon-all on a post-surgery MRI scan. Because of the resection area FreeSurfer did not include certain parts which should be included. What is the correct way of correcting this? I thought about editing the wm.mgz file by adding missing white matter using a brush value of 255 and erase white matter with a value of 1. Followed by re-creating the surfaces using: recon-all -autorecon2-wm -autorecon3 -subjid ... Thank you very much. Best Regards, Michael [image: fs.png]

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