[Freesurfer] where to find label values of Hippocampus Segmentation v6.0
External Email - Use Caution Hello Freesurfer developers, this is just a quick question: where/with what function can I get all the label values that are included in lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz and rh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz I want to replace the HIP labels in the Brainnetome segmentation with the freesurfer 6.0 ones, for this I need this information. I can not find it in the publication or in the freesurfer color LUT. Thank you very much in advance! Carolin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Projecting a subcortical label to the surface
External Email - Use Caution Hello FreeSurfer users, I have a subcortical segmentation that I want to project to the nearest cortical vertex. Would I use the mri_vol2surf command to accomplish this, or do I need to convert the segmentation into a label, then project the label to the fsaverage cortical surface? Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freeview update error
External Email - Use Caution Hi Kelly, you can try yum install qt5-qtbase-gui qt5-qtwebkit qt5-qtwebkit-devel And if it still doesn't work, you can try yum install harfbuzz On Mon, Apr 22, 2019 at 9:05 AM Kelly Vaughn wrote: > External Email - Use Caution > > Hello FreeSurfer community, > > I believe I have installed both freetype and freetype-devel now. > I now get a new error, that is similar, but may have a slightly different > solution: > > Freeview:symbol lookup error: > /usr/local/freesurfer/bin/../lib/qt/lib/libQt5Gui.so.5: undefined symbol: > hb_font_funcs_set_font_h_extents_func > > Does anyone have any advice regarding this error? > > 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev-20190416-14809f1 > 2) Platform: Red Hat Enterprise Linux 7 > > On Wed, Apr 17, 2019 at 3:06 PM Kelly Vaughn > wrote: > >> Thank you for your help! >> >> When I look within /usr/lib64 (using ls *libfreetype*) , I see: >> lib64/libfreetype.so.6 lib64/libfreetype.so.6.10.0 >> >> When I type: >> strings /usr/lib64/libfreetype.so.6 | grep -i ft_get_font_format >> I do not get any output. >> >> When I type: >> sudo yum install freetype.x86_64 freetype-devel.x86_64 >> the first package installs, but I get the following error message for the >> second package: >> No package freetype-devel.x86_64 available. >> Error: Nothing to do >> >> I have seen these types of errors on this computer many times when I try >> to install or use different programs, so I understand if it is not actually >> a FreeSurfer problem. If anyone has any advice, I would love to hear it. >> I'll continue to try to solve it on my own as well. >> >> On Wed, Apr 17, 2019 at 2:03 PM fsbuild wrote: >> >>> Hello Kelly, >>> >>> Do you have libfreetype installed on your system (which defines that >>> symbol)? >>> >>> $ strings /usr/lib64/libfreetype.so.6 | grep -i ft_get_font_format >>> FT_Get_Font_Format >>> >>> If not, you can install it with, >>> >>> $ sudo yum install freetype.x86_64 freetype-devel.x86_64 >>> >>> - R. >>> >>> On Apr 17, 2019, at 10:09, Kelly Vaughn >>> wrote: >>> >>> libQt5XcbQpa.so.5: undefined symbol: FT_Get_Font_Format >>> >>> >>> >> >> -- >> Kelly Vaughn, Ph.D. >> Postdoctoral Research Fellow >> Children's Learning Institute >> > > > -- > Kelly Vaughn, Ph.D. > Postdoctoral Research Fellow > Children's Learning Institute > ___ > 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] freeview and complex values
Hi Shahin, Freeview does not support color wheel colormap yet. We will add that option very soon. Best, Ruopeng On 4/22/19 2:52 PM, sha...@nmr.mgh.harvard.edu wrote: > Hi Surfers, > I am trying to use freeview to present retinotopy mapping in > subcortical regions. I need to show complex (real and imag) values > generated by a retinotopy analysis in a 'color wheel' format (similar > to what tksurfer does). > > Any hint? > > > _ > > Shahin Nasr > > Assistant Prof. in Radiology > Harvard Medical School > Martinos Imaging Center, MGH > Bldg 149, 13th street, > Charlestown, MA 02129 > > ___ > 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 and complex values
Hi Surfers, I am trying to use freeview to present retinotopy mapping in subcortical regions. I need to show complex (real and imag) values generated by a retinotopy analysis in a 'color wheel' format (similar to what tksurfer does). Any hint? _ Shahin Nasr Assistant Prof. in Radiology Harvard Medical School Martinos Imaging Center, MGH Bldg 149, 13th street, Charlestown, MA 02129 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_surf2surf help
External Email - Use Caution I am still having an issue with the command. This is what I am running: (MRI_DIR is the subj/mri, and SURF_DIR is the subj/surf directory) tkregister2 --mov /rawavg.mgz --targ /orig.mgz --reg /register.native.dat --noedit --regheader mri_surf2surf --sval-xyz pial --reg /register.native.dat /rawavg.mgz --hemi lh --tval /lh.native.pial --tval-xyz /rawavg.mgz --s Currently, the surface is centered inside the brain image (rawavg.mgz), but it is rotated and not oriented correctly. Perhaps I am missing a step. Thanks, Katie From: Larson, Kathleen E Sent: Tuesday, April 16, 2019 2:15 PM To: Freesurfer support list Subject: RE: [Freesurfer] mri_surf2surf help Thank you! Yes, I was able to figure it out. However, even when I swap the moving/target inputs, the surface is still not in the correct anatomical space. Also, just so you are aware, the instructions on the website you gave me aren't up to date... the --tval-xyz requires a volume input, but the instructions don't include one, so it you run it exactly like it is there you'll get an error. Thanks, Katie From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D. [dgr...@mgh.harvard.edu] Sent: Thursday, April 11, 2019 10:37 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_surf2surf help You are almost there. You need to swap mov and targ in your tkregister2 command. I also found these instructions on how to do this, but you seemed to have figured it out already https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnatdata=02%7C01%7Ckathleen.e.larson%40vanderbilt.edu%7C94991fa8b1e549ea2c9e08d6be93b12c%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636905938873837930sdata=K40k6eVZ40ejC4tNfOrgL%2BWhb6Zh%2FqJwQtpVzpgYM9s%3Dreserved=0 On 4/10/19 6:38 PM, Larson, Kathleen E wrote: > External Email - Use Caution > > Thanks. I'm now able to run the command without error. However, the surface > output is not lined up with the original image that I used as the FS input. > Here is the code I use: > > tkregister2 --mov orig.mgz --targ rawavg.mgz --reg register.native.dat --s > $subject > mri_surf2surf --reg register.native.dat rawavg.mgz --hemi lh --sval-xyz pial > --tval-xyz rawavg.mgz --tval ./lh.native.pial --s SUBJECT_ID > > My guess is that I am somehow not creating the proper transform... do you see > anything here that I should be doing differently? > > Thanks, > Katie > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D. > [dgr...@mgh.harvard.edu] > Sent: Monday, April 08, 2019 12:27 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_surf2surf help > > Have you looked at the help? Run with --help and look at example 4 > doug > > On 4/4/19 9:56 PM, Larson, Kathleen E wrote: >> External Email - Use Caution >> >> Hello FreeSurfer developers, >> >> I'm having trouble running the command mri_surf2surf, and I haven't >> been able to find a fix in the message archives (a similar question >> has been asked, but I couldn't find the answer). I am trying to >> convert the pial and white matter surfaces for a series of subjects >> back to the anatomical space. I have computed the registration matrix >> to transform the surfaces, but am having trouble with the >> mri_surf2surf syntax. This is the command I am trying to run: >> >> mri_surf2surf --hemi lh --sval-xyz pial --reg register.native.dat >> rawavg.mgz --tval lh.pial.native --tval-xyz --s >> >> and I get an error saying that --tval-xyz requires an input volume. >> (The syntax described on the website >> (https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsAnat-to-NativeAnatdata=02%7C01%7Ckathleen.e.larson%40vanderbilt.edu%7C94991fa8b1e549ea2c9e08d6be93b12c%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636905938873837930sdata=K40k6eVZ40ejC4tNfOrgL%2BWhb6Zh%2FqJwQtpVzpgYM9s%3Dreserved=0) >> is >> out of date.) I have tried to use rawavg.mgz as the input volume, but >> then I get an output that can only be read as a scalar overlay, and I >> need an actual surface. When I try to use a surface as the input, I >> get an error saying that the file type cannot identified. >> >> Do you have any suggestions for what I am doing wrong? >> >> Thank you, >> >> Kathleen Larson >> Department of Biomedical Engineering >> Vanderbilt University >> 304 Featheringill-Jacobs Hall >> (425)-894-2005 >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >>
[Freesurfer] mri_vol2surf error
External Email - Use Caution Hello FS users, I am having a problem with mri_vol2surf. I want to project subcortical voxels onto the cortical surface. I found out that I can do this with the mri_vol2surf command. I am following the example given on the documentation, but I am getting this error: mri_vol2surf: could not read surface /working/ABCD/FS2/7583b4bc-b8fc-4390-8504-1a495b70d2bc//surf/lh.white. I am trying to project to the surface of the fsaverage. Does this error mean that FS is unable to find the fsaverage surface? Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] thresholded cluster output data
External Email - Use Caution Hi Everyone, I'm new to freesurfer, and I was wondering if there is a way to output clusterwise threshold from Freeview (or any other tool) to illustrate cluster size, location, and significance? I understand that mri_glmfit-sim outputs cluster data after multiple cluster correction, but I was wondering if there is a way to get a similar cluster output prior to running multiple cluster correction. Thank you, DP ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freeview update error
External Email - Use Caution Hello FreeSurfer community, I believe I have installed both freetype and freetype-devel now. I now get a new error, that is similar, but may have a slightly different solution: Freeview:symbol lookup error: /usr/local/freesurfer/bin/../lib/qt/lib/libQt5Gui.so.5: undefined symbol: hb_font_funcs_set_font_h_extents_func Does anyone have any advice regarding this error? 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev-20190416-14809f1 2) Platform: Red Hat Enterprise Linux 7 On Wed, Apr 17, 2019 at 3:06 PM Kelly Vaughn wrote: > Thank you for your help! > > When I look within /usr/lib64 (using ls *libfreetype*) , I see: > lib64/libfreetype.so.6 lib64/libfreetype.so.6.10.0 > > When I type: > strings /usr/lib64/libfreetype.so.6 | grep -i ft_get_font_format > I do not get any output. > > When I type: > sudo yum install freetype.x86_64 freetype-devel.x86_64 > the first package installs, but I get the following error message for the > second package: > No package freetype-devel.x86_64 available. > Error: Nothing to do > > I have seen these types of errors on this computer many times when I try > to install or use different programs, so I understand if it is not actually > a FreeSurfer problem. If anyone has any advice, I would love to hear it. > I'll continue to try to solve it on my own as well. > > On Wed, Apr 17, 2019 at 2:03 PM fsbuild wrote: > >> Hello Kelly, >> >> Do you have libfreetype installed on your system (which defines that >> symbol)? >> >> $ strings /usr/lib64/libfreetype.so.6 | grep -i ft_get_font_format >> FT_Get_Font_Format >> >> If not, you can install it with, >> >> $ sudo yum install freetype.x86_64 freetype-devel.x86_64 >> >> - R. >> >> On Apr 17, 2019, at 10:09, Kelly Vaughn wrote: >> >> libQt5XcbQpa.so.5: undefined symbol: FT_Get_Font_Format >> >> >> > > -- > Kelly Vaughn, Ph.D. > Postdoctoral Research Fellow > Children's Learning Institute > -- Kelly Vaughn, Ph.D. Postdoctoral Research Fellow Children's Learning Institute ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] CORRECTING DEFECT 1 problem
Hi Ruwan have you looked at the data? Can you tell us what the acquisition parameters are or send us a 3-plane image of the norm.mgz with the lh.orig.nofix and rh.orig.nofix surfaces? The big defects are usually a symptom of something else cheers Bruce On Mon, 22 Apr 2019, Pradeepa Ruwan wrote: External Email - Use Caution Dear Freesurfer experts, I frequently get correcting defect error. It seems freezing the recon-all after the defect and it won't run thereafter. Due to this error, I can not use most of the data for connectome analysis. Can you please tell me how to get rid of this? I have attached a picture FYI. Best regards, Ruwan On Mon, Apr 22, 2019 at 11:10 AM Bruce Fischl wrote: sorry, I've been traveling On Mon, 22 Apr 2019, Abby tang wrote: > > External Email - Use Caution > > Hi BruceI did't get your reply message yet. I have send the subject file to you. Could you give me > your advises? > Thank you for your help. > Abby > > Abby tang 于2019年4月19日周五 上午8:32写道： > Hello，BruceI attached my subjects. Please help me. > Thank you. > Abby > [icon_10_generic_list.png] 2851A_T1_w4.nii[IMAGE] > > Bruce Fischl 于2019年4月18日周四 下午10:53写道： > Hi Abby > > it's hard to tell from the image, but it looks like there is a big I/S > bias field as well as large amounts of pathology. > > If you upload the subject to our ftp site we will take a look > > cheers > Bruce > On Thu, 18 Apr > 2019, Abby > tang wrote: > > > > > External Email - Use Caution > > > > Hello FreeSurfer Developers, > > > > I'm attempting to recon_all my subjects which is .nii file. But I usually meet > this error. > > > > CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950) > > After retessellation of defect 0 (v0=950), euler #=20 (87340,255044,167724) : > difference with theory > > (-32) = -52 > > > > CORRECTING DEFECT 1 (vertices=46367, convex hull=8524, v0=962) > > Segmentation fault (core dumped) > > Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13 10:44:52 > UTC 2019 x86_64 x86_ > > 64 x86_64 GNU/Linux > > > > recon-all -s 2851A_T1_w4 exited with ERRORS at Thu Apr 18 20:25:16 CST 2019 > > > > To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > I check files in blow command and attached picture. > > > > freeview -v 2851A_T1_w4/mri/norm.mgz -f 2851A_T1_w4/surf/lh.orig.nofix > 2851A_T1_w4/surf/lh.inflated. > > nofix > > > > almost all of subjects go wrong. I need your help. > > > > please give some advises with program statements in detail. > > > > I really appreciate your help > > > > 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz > > 2) Platform: ubuntu 18 > > 3) recon-all.log:see attached > > > >___ > 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] Problems with recon-all -s soft and hard fallures
External Email - Use Caution Dear Greve, Please can you let me know if you got the two folders of data I sent you? Best regards Ileana Camerino PhD candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognition Spinozabuilding Room B02.25 Montessorilaan 3, 6525 HR Nijmegen The Netherlands Tel. +31-24 3612618 On 16/04/2019, 21:14, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D." wrote: Unfortunately, it usually means that you need to go in and manually fix the problems that you are seeing. Probably the best thing is to look at the aseg.presurf.mgz to see how the WM lesions are getting labeled. You may have to go in an label them manually. Can you upload a case or two here ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming On 4/16/19 11:05 AM, Camerino, .I.L. (Ileana) wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > > I am running recon all from the terminal of a linux machine: > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. > > > I tried recon all on an image dataset of small vessel disease > patients. I tried the command on several subjects and I got the same > outcome: a soft fallure. > > Please, find the recon all log in the attachment. > > Even though in the "recon all.log": it says: recon-all -s sub025 > finished without errors, after checking the pial and white matter > segmentations, very clear misplacement failures and part of dura mater > are present (see attachment: segmenation misplacement and dura). > > > I am also wandering how to avoid that white matter lesions are taken > into the aseg segmentation? > > > I checked the documentation and this kind of errors is not mentioned > anywhere. Can be the case, that this error is due to the fact that > these are clinical images? Can this problem be fixed? > > > For sake of curiosity, I tried the recon all command on another > dataset (stroke) and with these data I got an hard failure. > > recon all exited with errors: > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > ***FAILED*** (p=0.0573, pval=0.0034 < threshold=0.0050). (see second > recon all o35403143 with errors) > > > Please, can anyone give me some ideas how to fix both errors? > > Thank you in advance > > Ileana > > > ___ > 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] CORRECTING DEFECT 1 problem
External Email - Use Caution Dear Freesurfer experts, I frequently get correcting defect error. It seems freezing the recon-all after the defect and it won't run thereafter. Due to this error, I can not use most of the data for connectome analysis. Can you please tell me how to get rid of this? I have attached a picture FYI. Best regards, Ruwan On Mon, Apr 22, 2019 at 11:10 AM Bruce Fischl wrote: > sorry, I've been traveling > On Mon, 22 Apr 2019, Abby tang wrote: > > > > > External Email - Use Caution > > > > Hi BruceI did't get your reply message yet. I have send the subject > file to you. Could you give me > > your advises? > > Thank you for your help. > > Abby > > > > Abby tang 于2019年4月19日周五 上午8:32写道： > > Hello，BruceI attached my subjects. Please help me. > > Thank you. > > Abby > > [icon_10_generic_list.png] 2851A_T1_w4.nii[IMAGE] > > > > Bruce Fischl 于2019年4月18日周四 下午10:53写道： > > Hi Abby > > > > it's hard to tell from the image, but it looks like there is a big > I/S > > bias field as well as large amounts of pathology. > > > > If you upload the subject to our ftp site we will take a look > > > > cheers > > Bruce > > On Thu, 18 Apr > > 2019, Abby > > tang wrote: > > > > > > > > External Email - Use Caution > > > > > > Hello FreeSurfer Developers, > > > > > > I'm attempting to recon_all my subjects which is .nii file. But > I usually meet > > this error. > > > > > > CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950) > > > After retessellation of defect 0 (v0=950), euler #=20 > (87340,255044,167724) : > > difference with theory > > > (-32) = -52 > > > > > > CORRECTING DEFECT 1 (vertices=46367, convex hull=8524, v0=962) > > > Segmentation fault (core dumped) > > > Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu SMP Wed > Mar 13 10:44:52 > > UTC 2019 x86_64 x86_ > > > 64 x86_64 GNU/Linux > > > > > > recon-all -s 2851A_T1_w4 exited with ERRORS at Thu Apr 18 > 20:25:16 CST 2019 > > > > > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > I check files in blow command and attached picture. > > > > > > freeview -v 2851A_T1_w4/mri/norm.mgz -f > 2851A_T1_w4/surf/lh.orig.nofix > > 2851A_T1_w4/surf/lh.inflated. > > > nofix > > > > > > almost all of subjects go wrong. I need your help. > > > > > > please give some advises with program statements in detail. > > > > > > I really appreciate your help > > > > > > 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz > > > 2) Platform: ubuntu 18 > > > 3) recon-all.log:see attached > > > > > >___ > > 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
