Re: [Freesurfer] recon-all -s SOME_SUBJECT exited with ERRORS
External Email - Use Caution Hello Developers! I am getting the same error in several patients (not all). The common error between all of them is this line Waiting for PID 2778 of (2778 2781) to complete... /usr/local/freesurfer/bin/reconbatchjobs: line 81: 2778 Segmentation fault (core dumped) exec $JOB >> $LOG 2>&1 Waiting for PID 2781 of (2778 2781) to complete... Any idea? Thanks in advance! Emanuel On Tue, Oct 1, 2019 at 5:07 PM Emanuel Alvaredo wrote: > Hello FreeSurfer Developers, > > I am running de following command > > /usr/local/freesurfer/subjects/SOME_SUBJECT > /usr/local/freesurfer/bin/recon-all > -s SOME_SUBJECT -i > /fleni/patients/KING_LUCAS_JAVIER_25-09-2019/2_COGNITIVO_FLENI/4_Accelerated_Ax_IR-FSPGR/i2750291.MRDC.58 > - > all -parallel > > > I've searched the list and no similar errors have been reported. Does anyone > have any thoughts on how to trouble-shoot this one? Also, Ive attached the > recon-all.log in case it's of any use. > I have checked the log but I dont find de cause. > > 1) FreeSurfer > version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > 2) Platform:Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz > 3) uname -a: Linux fisicos-ub2 5.0.0-29-generic #31~18.04.1-Ubuntu SMP Thu > Sep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux > 4) recon-all.log: see attached > > Thanks in advance > Emanuel > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all -s SOME_SUBJECT exited with ERRORS
External Email - Use Caution Hi Bruce, same result. Question, Is it possible run two recon-all at the same time? Emanuel On Thu, Nov 7, 2019 at 4:41 PM Bruce Fischl wrote: > hmmm, does it always happen for this subject? What if you don't use > -parallel? > On Thu, 7 Nov 2019, Emanuel Alvaredo wrote: > > > > > External Email - Use Caution > > > > Hi Bruce! Thanks for answer!! > > * The command line is > > > > recon-all -s SUBJECT_NAME -i > > > /patients/SUBJECT_NAME/2_COGNITIVO/4_Accelerated_Ax_IR-FSPGR/i1602413.MRDC.127 > -all -parallel > > > > > > > > * In this mail is attached the log. There is > > > > Segmentation fault (core dumped) > > > > * This happens running when I call a process from a Java application, > but too if I run the > > command manually. > > > > > > > > I think this is the problem, but I dont know why. > > > > Thanks in advance > > > > > > Emanuel > > > > > > On Wed, Oct 30, 2019 at 10:51 AM Bruce Fischl < > fis...@nmr.mgh.harvard.edu> wrote: > > Hi Emanuel > > > > can you give us more details. What was your command line? What was > the > > full job output? What is in the recon-all.log? Does this happen if > you > > run directly instead of through some type of batch server? > > > > cheers > > Bruce > > On Wed, 30 Oct > > 2019, Emanuel Alvaredo wrote: > > > > > > > > External Email - Use Caution > > > > > > Hello Developers! > > > I am getting the same error in several patients (not all). The > common error > > > between all of them is this line > > > > > > Waiting for PID 2778 of (2778 2781) to complete... > > > /usr/local/freesurfer/bin/reconbatchjobs: line 81: 2778 > Segmentation fault > > > (core dumped) exec $JOB >> $LOG 2>&1 > > > Waiting for PID 2781 of (2778 2781) to complete... > > > > > > Any idea? > > > > > > Thanks in advance! > > > > > > > > > > > > Emanuel > > > > > > > > > On Tue, Oct 1, 2019 at 5:07 PM Emanuel Alvaredo < > ealvar...@gmail.com> wrote: > > > > > > Hello FreeSurfer Developers, > > > > > > I am running de following command > > > /usr/local/freesurfer/subjects/SOME_SUBJECT > > > /usr/local/freesurfer/bin/recon-all > > > -s SOME_SUBJECT -i > /fleni/patients/KING_LUCAS_JAVIER_25-09-2019/2_COGNITIVO_ > > > FLENI/4_Accelerated_Ax_IR-FSPGR/i2750291.MRDC.58 - > > > all -parallel > > > I've searched the list and no similar errors have been reported. > Does anyone > > > have any thoughts on how to trouble-shoot this one? Also, Ive > attached the > > > recon-all.log in case it's of any use. > > > I have checked the log but I dont find de cause. > > > > > > 1) FreeSurfer > version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb > > > 96c > > > 2) Platform:Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz > > > 3) uname -a: Linux fisicos-ub2 5.0.0-29-generic > #31~18.04.1-Ubuntu SMP Thu S > > > ep 12 18:29:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux > > > 4) recon-all.log: see attached > > > Thanks in advance > > > Emanuel > > > > > > > > >___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Freeview: Load multiples overlays for one surface
External Email - Use Caution Hi! I would like from command line to open one surface with multiple ovelays. For example, intead of this ..-f surf/lh.inflated:overlay=surf/lh.sulc surf/lh.inflated:overlay=surf/lh.thickness:overlay_threshold=1,5 I would like to do something like that -f surf/lh.inflated:overlay=surf/lh.sulc,overlay=surf/lh.thickness:overlay_threshold=1,5 is this possible? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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.
Re: [Freesurfer] Freeview: Load multiples overlays for one surface
External Email - Use Caution It's works! Thanks a lot! El vie., 7 sept. 2018 a las 16:46, Ruopeng Wang () escribió: > Yes, it is possible. But you should use ':' as separator like this: > > -f > surf/lh.inflated:overlay=surf/lh.sulc:overlay=surf/lh.thickness:overlay_threshold=1,5 > > Ruopeng > > On 09/07/2018 03:11 PM, Emanuel Alvaredo wrote: > > External Email - Use Caution > > Hi! I would like from command line to open one surface with multiple > ovelays. For example, intead of this > > ..-f surf/lh.inflated:overlay=surf/lh.sulc > surf/lh.inflated:overlay=surf/lh.thickness:overlay_threshold=1,5 > > I would like to do something like that > > -f > surf/lh.inflated:overlay=surf/lh.sulc,overlay=surf/lh.thickness:overlay_threshold=1,5 > > > is this possible? > > Thanks! > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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 . 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. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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.
[Freesurfer] Error in running make_average_subject
External Email - Use Caution Hello!, I am getting the following error using the command make_average_subject mri/norm.mgz: could not load norm volume from (null) I have found this page with a path for de issue https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html But I dont know how to apply the path. Can you give some information about this? Thanks! Emanuel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error in running make_average_subject
External Email - Use Caution Thanks Bruce. The following is the command. make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects subject1 subject2 subject3 And I made a mistake in may last mail. I use the word path instead of patch I have found this page with a *patch* for de issue https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html But I dont know how to apply the *patch*. Can you give some information about this? Emanuel On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl wrote: > Hi Emanuel > > you need to send us the full command you ran and output of it if you want > us to be able to help you > > cheers > Bruce > On Fri, 7 Dec 2018, Emanuel Alvaredo wrote: > > > > > External Email - Use Caution > > > > Hello!, I am getting the following error using the > command make_average_subject > > > > mri/norm.mgz: could not load norm volume from (null) > > > > I have found this page with a path for de issue > > > > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html > > > > But I dont know how to apply the path. Can you give some information > about this? > > > > Thanks! > > > > > > > > Emanuel > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error in running make_average_subject
External Email - Use Caution Thanks for your answer Douglas. I replaced the make_average_surface file with the new one but I have the same message error. ASeg Vox2RAS: --- -1.0 0.0 0.0 128.0; 0.0 0.0 1.0 -128.0; 0.0 -1.0 0.0 128.0; 0.0 0.0 0.0 1.0; mghRead(mri/norm.mgz, -1): could not open file - Labeling Slice relabeling unlikely voxels in interior of white matter mri/norm.mgz: could not load norm volume from (null) Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:16:02 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Thanks Emanuel On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > Sorry, the disk that held that patch failed and we did not have a backup > so not everything was restored. I just put this file there: > > > https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface > > Copy it to $FREESURFER_HOME/bin. Let me know how it goes > > > On 12/10/18 12:48 PM, Emanuel Alvaredo wrote: > > External Email - Use Caution > Thanks Bruce. The following is the command. > > > make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects > subject1 subject2 subject3 > > > And I made a mistake in may last mail. I use the word path instead of patch > > I have found this page with a *patch* for de issue > > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html > > But I dont know how to apply the *patch*. Can you give some information > about this? > > > Emanuel > > > On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl > wrote: > >> Hi Emanuel >> >> you need to send us the full command you ran and output of it if you want >> us to be able to help you >> >> cheers >> Bruce >> On Fri, 7 Dec 2018, Emanuel Alvaredo wrote: >> >> > >> > External Email - Use Caution >> > >> > Hello!, I am getting the following error using the >> command make_average_subject >> > >> > mri/norm.mgz: could not load norm volume from (null) >> > >> > I have found this page with a path for de issue >> > >> > >> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html >> > >> > But I dont know how to apply the path. Can you give some information >> about this? >> > >> > Thanks! >> > >> > >> > >> > Emanuel >> > >> >___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error in running make_average_subject
External Email - Use Caution Hello Bruce, thanks for your anwer. Sure. The command is *make_average_subject --out avgsubjectPRUEBAESTASI! --subjects Bartley_Recon Baez_Recon Bonilla_Recon* The output is in the attached file Thanks! Emanuel On Wed, Dec 12, 2018 at 7:05 PM Bruce Fischl wrote: > Hi Emanuel, > > can you include the full command line and output? > > cheers > Bruce > On Wed, 12 Dec 2018, > Emanuel Alvaredo wrote: > > > > > External Email - Use Caution > > > > Thanks for your answer Douglas. I replaced the make_average_surface > file with the new one but I > > have the same message error. > > ASeg Vox2RAS: --- > > -1.0 0.0 0.0 128.0; > > 0.0 0.0 1.0 -128.0; > > 0.0 -1.0 0.0 128.0; > > 0.0 0.0 0.0 1.0; > > mghRead(mri/norm.mgz, -1): could not open file > > - > > > > Labeling Slice > > relabeling unlikely voxels in interior of white matter > > mri/norm.mgz: could not load norm volume from (null) > > > > Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 > 17:16:02 UTC 2018 x86_64 x86_64 > > x86_64 GNU/Linux > > > > Thanks > > > > Emanuel > > > > > > On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> wrote: > > Sorry, the disk that held that patch failed and we did not have a > backup so not > > everything was restored. I just put this file there: > > > > > https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface > > > > Copy it to $FREESURFER_HOME/bin. Let me know how it goes > > > > > > On 12/10/18 12:48 PM, Emanuel Alvaredo wrote: > > > > External Email - Use Caution > > > > Thanks Bruce. The following is the command. > > > > make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects > subject1 > > subject2 subject3 > > > > > > And I made a mistake in may last mail. I use the word path instead of > patch > > > > I have found this page with a patch for de issue > > > > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html > > > > But I dont know how to apply the patch. Can you give some information > about this? > > > > > > Emanuel > > > > > > On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl > wrote: > > Hi Emanuel > > > > you need to send us the full command you ran and output of it if > you want > > us to be able to help you > > > > cheers > > Bruce > > On Fri, 7 Dec 2018, Emanuel Alvaredo wrote: > > > > > > > > External Email - Use Caution > > > > > > Hello!, I am getting the following error using the > > command make_average_subject > > > > > > mri/norm.mgz: could not load norm volume from (null) > > > > > > I have found this page with a path for de issue > > > > > > > > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html > > > > > > But I dont know how to apply the path. Can you give some > information about > > this? > > > > > > Thanks! > > > > > > > > > > > > Emanuel > > > > > >___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Wed Dec 12 15:07:35 -03 2018 /usr/local/freesurfer/subjects/avgsubjectPRUEBAESTASI! /usr/local/freesurfer/bin/recon-all -s avgsubjectPRUEBAESTASI! -cortribbon -aparc2aseg subjid avgsubj
[Freesurfer] Custom Colormap
External Email - Use Caution Hello! I would like to ask you about customs colormaps. I have created my own FreeSurferColorLUT.txt and I would like configure the color map using command line. Is it possible? Thanks in advance. Emanuel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Custom Colormap
External Email - Use Caution Thanks for the answer Bruce. Is For segmentations. I have run freesurfer for 100 nomal patients. I have calculated standard desviation and mean, then I am comparing the results against a patological patient. So, I would like to open freeview, for example with this command freeview -v mri/orig.mgz -f surf/lh.white:edgecolor=blue surf/lh.pial:edgecolor=red surf/rh.white:edgecolor=blue surf/rh.pial:edgecolor=red surf/rh.inflated:overlay=surf/rh.w-g.pct.mgh:overlay_threshold=0,60:overlay_color=colorwheel,inverse:overlay=surf/rh.sulc:overlay_threshold=-13,13:overlay_color=colorwheel,inverse:overlay=surf/rh.thickness:overlay_threshold=1,5:overlay_color=colorwheel,inverse surf/lh.inflated:overlay=surf/lh.w-g.pct.mgh:overlay_threshold=0,60:overlay_color=colorwheel,inverse:overlay=surf/lh.sulc:overlay_threshold=-13,13:overlay_color=colorwheel,inverse:overlay=surf/lh.thickness:overlay_threshold=1,5:overlay_color=colorwheel,inverse and show in my custom colores in segments. Emanuel On Mon, Apr 1, 2019 at 11:17 AM Bruce Fischl wrote: > Hi Emanuel > > can you tell us more. For parellations or segmentations? Are you just > changing the color of existing parcels/segments? If so you can just > import it in freeview > cheers > Bruce > > On Mon, 1 Apr 2019, Emanuel Alvaredo wrote: > > > > > External Email - Use Caution > > > > Hello! > > I would like to ask you about customs colormaps. I have created my > > own FreeSurferColorLUT.txt and I would like configure the color map > using command line. > > Is it possible? > > > > Thanks in advance. > > > > Emanuel > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Custom Colormap
External Email - Use Caution Thanks Bruce, Do you know what is the command line option? Thanks! Emanuel On Mon, Apr 1, 2019 at 11:34 AM Bruce Fischl wrote: > I see. You can give freeview a custom lookup table on the command line > > cheers > Bruce > > > On Mon, 1 Apr 2019, Emanuel Alvaredo wrote: > > > > > External Email - Use Caution > > > > Thanks for the answer Bruce. > > Is For segmentations. I have run freesurfer for 100 nomal patients. I > have calculated > > standard desviation and mean, then I am comparing the results against a > patological > > patient. So, I would like to open freeview, for example with this command > > > > freeview -v mri/orig.mgz -f surf/lh.white:edgecolor=blue > surf/lh.pial:edgecolor=red > > surf/rh.white:edgecolor=blue > > surf/rh.pial:edgecolor=red > > > surf/rh.inflated:overlay=surf/rh.w-g.pct.mgh:overlay_threshold=0,60:overlay_color=colorwhe > > > el,inverse:overlay=surf/rh.sulc:overlay_threshold=-13,13:overlay_color=colorwheel,inverse: > > > overlay=surf/rh.thickness:overlay_threshold=1,5:overlay_color=colorwheel,inverse > > > surf/lh.inflated:overlay=surf/lh.w-g.pct.mgh:overlay_threshold=0,60:overlay_color=colorwhe > > > el,inverse:overlay=surf/lh.sulc:overlay_threshold=-13,13:overlay_color=colorwheel,inverse: > > > overlay=surf/lh.thickness:overlay_threshold=1,5:overlay_color=colorwheel,inverse > > > > and show in my custom colores in segments. > > > > > > > > > > Emanuel > > > > > > On Mon, Apr 1, 2019 at 11:17 AM Bruce Fischl > wrote: > > Hi Emanuel > > > > can you tell us more. For parellations or segmentations? Are you > just > > changing the color of existing parcels/segments? If so you can just > > import it in freeview > > cheers > > Bruce > > > > On Mon, 1 Apr 2019, Emanuel Alvaredo wrote: > > > > > > > > External Email - Use Caution > > > > > > Hello! > > > I would like to ask you about customs colormaps. I have created > my > > > own FreeSurferColorLUT.txt and I would like configure the color > map using > > command line. > > > Is it possible? > > > > > > Thanks in advance. > > > > > > Emanuel > > > > > >___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Custom Colormap
External Email - Use Caution Thanks! Emanuel On Mon, Apr 1, 2019 at 12:13 PM Ruopeng Wang wrote: > Hi Emanuel, > > You can use this command to load customized color table file: > > freeview -v brain.mgz:colormap=lut:lut=color_table_file.txt > > Best, > Ruopeng > On 4/1/19 10:40 AM, Emanuel Alvaredo wrote: > > Thanks Bruce, Do you know what is the command line option? > Thanks! > Emanuel > > > On Mon, Apr 1, 2019 at 11:34 AM Bruce Fischl > wrote: > >> I see. You can give freeview a custom lookup table on the command line >> >> cheers >> Bruce >> >> >> On Mon, 1 Apr 2019, Emanuel Alvaredo wrote: >> >> > >> > External Email - Use Caution >> > >> > Thanks for the answer Bruce. >> > Is For segmentations. I have run freesurfer for 100 nomal patients. I >> have calculated >> > standard desviation and mean, then I am comparing the results against a >> patological >> > patient. So, I would like to open freeview, for example with this >> command >> > >> > freeview -v mri/orig.mgz -f surf/lh.white:edgecolor=blue >> surf/lh.pial:edgecolor=red >> > surf/rh.white:edgecolor=blue >> > surf/rh.pial:edgecolor=red >> > >> surf/rh.inflated:overlay=surf/rh.w-g.pct.mgh:overlay_threshold=0,60:overlay_color=colorwhe >> > >> el,inverse:overlay=surf/rh.sulc:overlay_threshold=-13,13:overlay_color=colorwheel,inverse: >> > >> overlay=surf/rh.thickness:overlay_threshold=1,5:overlay_color=colorwheel,inverse >> > >> surf/lh.inflated:overlay=surf/lh.w-g.pct.mgh:overlay_threshold=0,60:overlay_color=colorwhe >> > >> el,inverse:overlay=surf/lh.sulc:overlay_threshold=-13,13:overlay_color=colorwheel,inverse: >> > >> overlay=surf/lh.thickness:overlay_threshold=1,5:overlay_color=colorwheel,inverse >> > >> > and show in my custom colores in segments. >> > >> > >> > >> > >> > Emanuel >> > >> > >> > On Mon, Apr 1, 2019 at 11:17 AM Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> wrote: >> > Hi Emanuel >> > >> > can you tell us more. For parellations or segmentations? Are you >> just >> > changing the color of existing parcels/segments? If so you can >> just >> > import it in freeview >> > cheers >> > Bruce >> > >> > On Mon, 1 Apr 2019, Emanuel Alvaredo wrote: >> > >> > > >> > > External Email - Use Caution >> > > >> > > Hello! >> > > I would like to ask you about customs colormaps. I have >> created my >> > > own FreeSurferColorLUT.txt and I would like configure the >> color map using >> > command line. >> > > Is it possible? >> > > >> > > Thanks in advance. >> > > >> > > Emanuel >> > > >> > >___ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> >___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
