Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Recon-all error output
by Frank Chau 22 Jun '20

22 Jun '20

External Email - Use Caution Dear Freesurfer experts, I ran Recon-all on a batch of subject. Only one Recon-all error results were generated which the process just last for few minutes. There just 2 mgz file in mri folder of the subject output directory were generated. I re-run recon-all on the same subject, same result was got again. May I know the cause of this error? I upload the output result, log history and the T1.nii to the following share link, please feel free the check them: <https://www.dropbox.com/sh/lhbzct444n8ek8z/AADbtfyYEBNWZ4yYXPw7ejmwa?dl=0> https://www.dropbox.com/sh/lhbzct444n8ek8z/AADbtfyYEBNWZ4yYXPw7ejmwa?dl=0 Thank you. Regards Frank --------------------------- FRANK C Y CHAU Research assistant Division of Neurology Department of Medicine Tel: +852 6340 2553 Fax: 2872 5828 E-mail : cyfrank(a)hku.hk<mailto:cyfrank@hku.hk> Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong

2 1

Error with -qcache
by Mateus Aranha 22 Jun '20

22 Jun '20

External Email - Use Caution Dear FS team, I'm running -qcache on my subjects before group analysis and I get the following error for 2 of the subjects: ERROR: number of vertices in /home/neuroimagen7/Desktop/SoccerPlayers/ReconFiles/recon_T1/edits/ANON0266_recon_T1/surf/lh.thickness does not match surface (139424,138940) ERROR: reading curvature file The remaining subjects are fine! Thank you! Mateus

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Re: [Freesurfer] Freeview - Load custom overlay from terminal
by Loucao, Ricardo 22 Jun '20

22 Jun '20

External Email - Use Caution Hi Ruopeng, You were correct - for some reason the version I built was 2.0. I’ve downloaded a built version of freesurfer v7.1.0 and now I can successfully use the flag. Another question if I may: is there a way to toggle the “clear lower”/“clear higher” option also from the terminal? Thank you in advance! Best regards, Ricardo Date: Thu, 18 Jun 2020 13:28:56 +0000 From: "Wang, Ruopeng" <RWANG4(a)mgh.harvard.edu<mailto:RWANG4@mgh.harvard.edu>> Subject: Re: [Freesurfer] Freeview - Load custom overlay from terminal To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <FE2C8592-CFC2-41FD-9BB0-B4763CA86185(a)mgh.harvard.edu<mailto:FE2C8592-CFC2-41FD-9BB0-B4763CA86185@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" Hi Ricardo, The way you use the flag is correct. But have you made sure that you were actually running the latest version that you built? You can check freeview?s build time from About menu. Best, Ruopeng Date: Thu, 18 Jun 2020 08:15:44 +0000 From: "Loucao, Ricardo" <r.loucao(a)fz-juelich.de<mailto:r.loucao@fz-juelich.de>> Subject: [Freesurfer] Freeview - Load custom overlay from terminal 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>> Message-ID: <25D279E0-2256-47B0-B05A-1F470A1B3089(a)fz-juelich.de<mailto:25D279E0-2256-47B0-B05A-1F470A1B3089@fz-juelich.de>> Content-Type: text/plain; charset="utf-8" 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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

2 1

Re: [Freesurfer] recon-all for macaque brain
by Chris Klink 22 Jun '20

22 Jun '20

External Email - Use Caution Hi Minqing Jiang, Getting a macaque brain through Freesurfer requires a bit of manual tinkering. We have a description of how we do it on GitHub: https://github.com/VisionandCognition/NHP-Freesurfer There's also precon_all (https://github.com/recoveringyank/precon_all) which I haven't personally used yet, but I've seen results and it looks very promising! Good luck! Chris

1 0

How to make surface cuts / flatmaps. Alternative for tksurfer in 2020?
by Chris Klink 22 Jun '20

22 Jun '20

External Email - Use Caution How do people create flatmaps these days? It's getting more and more of a hassle to work with tksurfer (won't work on 64bit only Mac, throws tcl & tix errors on Linux in Freesurfer 7). I'm currently running tksurfer on Linux in FS6, that I basically only keep around for that purpose. I read on the mailing list that tkmedit and tksurfer are pretty much deprecated, but I've looked in Freeview and can't find a way to make cuts there. I must be missing something? Is there some other way of doing it? Should I dive into pycortex' Blender based approach? What are the options in 2020? Best, Chris

1 0

QDEC analyses
by xunzhang_hmrrc 21 Jun '20

21 Jun '20

External Email - Use Caution Hello Freesurfer developers, Recently, I have used QDEC of freesurfer 6.0.0 to examine the cortical thickness differences between two groups, and the manuscript has been submitted to a journal. One reviewer raised a question -"The manuscript stated that the right and left hemisphere were tested separately. Could the authors provide an explanation for this? I assume that testing over 68 (all ROIs) vs testing separately left and right (34 ROIs) would have an effect?" Unfornately, I don't know how to responde to this reviewer, so I would like to ask for your help. I just followed the tutorials of QDEC (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysisV6.0) and I found QDEC analyses have always be done for the two hemispheres separately. So, could you please provide some perspective and citation about the validation for such design of QDEC? Thank you in advance for your assistance, Best regards, Xun

2 2

QDEC analyses
by xunzhang_hmrrc 20 Jun '20

20 Jun '20

1 0

Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format
by Glasser, Matthew 19 Jun '20

19 Jun '20

External Email - Use Caution What kind of data does one display in an “OVERLAY” file? Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Katsumi, Yuta" <YKATSUMI(a)mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, June 18, 2020 at 5:43 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format 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 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

4 9

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.

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