Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

Custom LUT
by Benjamin Deck 31 May '22

31 May '22

External Email - Use Caution Hi freesurfer experts, I am attempting to create a custom LUT from a parcellation I created. I have projected the labels into the subject's volume space and then concatenated all of these volumtes together using: mri_concat --sum --f vols.txt --o sub_vols.mgz When I visualize these on the subject's t1w the number of ROIs looks approximately correct (n~105). However, my custom LUT seems to be incorrect. Not sure how that is. I used the FreesurferLUT as my template and added new colors and changed names of each row to match my file names (excluding the .mgz). Here is my custom LUT 0 Unknown 0 0 0 0 1 Net_10_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol 5 5 5 5 2 Net_10_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol 25 5 25 0 3 Net_11_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol 25 100 40 0 4 Net_11_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol 70 130 180 0 5 Net_12_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol 100 100 0 0 6 Net_12_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol 196 58 250 0 7 Net_12_ROIs_2_lh_native_sm6_sm6_dil2_lh_vol 100 25 0 0 8 Net_12_ROIs_2_rh_native_sm6_sm6_dil2_rh_vol 120 70 50 0 9 Net_13_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol 220 20 10 0 10 Net_13_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol 220 20 100 0 11 Net_13_ROIs_2_lh_native_sm6_sm6_dil2_lh_vol 180 40 120 0 12 Net_13_ROIs_2_rh_native_sm6_sm6_dil2_rh_vol 122 186 220 0 13 Net_13_ROIs_3_lh_native_sm6_sm6_dil2_lh_vol 140 20 140 0 14 Net_13_ROIs_3_rh_native_sm6_sm6_dil2_rh_vol 12 48 255 0 15 Net_13_ROIs_4_lh_native_sm6_sm6_dil2_lh_vol 20 30 140 0 ------and it goes on for 105 indices. here is my list of volumes Net_10_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_19_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_10_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_2_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_11_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_2_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_11_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_2_ROIs_2_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_12_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_2_ROIs_2_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_12_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_3_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_12_ROIs_2_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_3_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz -------and so on. Below I show that you can load each volume onto the brain and pick individual colors. [image: image.png] However, when I load the concatenated brain and load my custom image. All of ROIs get listed one of two ROIs. [image: image.png] Any guidance on this odd behavior would be much appreciated. Thanks, Ben OS: Windows--WSL2 Ubuntu 18 FS version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b -- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University* <https://secure-web.cisco.com/19Zn9eBKlEcFDurLHH9K8qOmPXm76HWXsKoN-XxABNV__4…> Virus-free. http://secure-web.cisco.com/17nfhwzVH4FamivxxfM5csvgLADzPjVc-AdC_7JKlsJRQMF… <https://secure-web.cisco.com/1E0laxvnp9bhVNgWasuocl4hqSjGHLHVu2yD3TqEvK6dfc…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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mri_normalize issues, Version 7
by Zoe O'Brien-Moran 31 May '22

31 May '22

External Email - Use Caution Hello FreeSurfer developers, I am attempting to run the mri_normalize function on T1 MPRAGE data and some of my subjects get an error: Iterating 2 times ------------- 3d normalization pass 1 of 2 error: No such file or directory error: MRInormFindControlPoints: could not find enough control points error: No such file or directory error: MRInormFindControlPoints failed This error comes up with some subjects but not others in the group with the same acquisition details. It is cross vendor (it has come up for both Siemens and Philips). Strangely enough, when I gave the data to someone else to run on their end, mri_normalize worked just fine... they are running FreeSurfer 5.3.0. On my own computer, running freesurfer version 7, I can get it to work by changing the orientation using mri_convert... though most subjects work with the original input orientation, and I would prefer not to have to do what feels like an arbitrary orientation change. Do you know why this could be happening? Were there any changes made to the mri_normalize function between v5.3.0 and v7? Thank you so much for any advice. Zoe O'Brien-Moran

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convert surface overlays to atlas
by Benjamin Deck 31 May '22

31 May '22

External Email - Use Caution Hi there freesurfer experts, I am fairly new to freesurfer. I am attempting to convert freesurfer overlay files and eventually create individual-specific annotation files which will then be used to create a segmentation file to be used for drawing white matter tracts. When I run mri_info on the overlay files I get the following: Volume information for Net_10_ROIs_1_lh.mgh type: MGH dimensions: 253237 x 1 x 1 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 253237.000 dof: 1 xstart: -126618.5, xend: 126618.5 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 1281.0000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 0.5000 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 1.0000 0.0000 0.0000 -126618.0000 0.0000 1.0000 0.0000 1280.5000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 1 ras to voxel transform: 1.0000 0.0000 0.0000 126618.0000 0.0000 1.0000 0.0000 -1280.5000 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 0.0000 1.0000 My initial thought was to run mri_label2label --> mri_label2vol --> mris_label2annot --mri_label2vol --> mri_concat = segmentation in native volume Running WSL2 Ubuntu 18_x86_64-7.2.0 FS: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b Any guidance would be greatly appreciated. Thank you! -- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University* <https://secure-web.cisco.com/1kz89t9S4HXvtMVxUekw-dPXLzzUcmmP6UBXoFUZuORVdR…> Virus-free. http://secure-web.cisco.com/1WixBPHZpnyB5-Xayd80a9TON-TvjqvK-WeaqazG-xtlOgj… <https://secure-web.cisco.com/1hU1RdFIRZigHPH9QSngZUY6qgxOLWWme7Djq567riRfsJ…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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convert .reg.lta linear transform to an ITK transform for 3DSlicer
by Gonzalo Rojas Costa 31 May '22

31 May '22

External Email - Use Caution Hi: How can I convert a .reg.lta linear transform to an ITK transform for 3DSlicer? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 https://secure-web.cisco.com/13TZ07AstA_Q_lsIF4aiCFiJWD-gpdMOlT0cLc-2oTVqOH… https://secure-web.cisco.com/16gO9CNWzQHT7IqdPqjexT9AfEDEQl7WrLvpp3Nc_AtMNw… https://secure-web.cisco.com/1gyom5cJyQ8cmW1-ISZiem0NN2me1FWbxC3aS-L8jw2c7m… http://secure-web.cisco.com/11hSSrxQ5y9JDhtiyawoQm5uEXQUx4ke5TYmqszpC-smAH4… https://secure-web.cisco.com/1VUiRWuUGVZcEiJxtLi98il3aVo2D9T3cokDDEuMEzwftN…

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Re: [Freesurfer] Freesurfer passowrd
by fsbuild 31 May '22

31 May '22

External Email - Use Caution Sending the info to your email shortly. - R. On May 31, 2022, at 05:38, nairulislam(a)tutamail.com wrote:        External Email - Use Caution        Hi there, I just downloaded the Freesurfer zip file that is meant to be used with the virtual box. I need the password of that zip file._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Virtual Box Password
by fsbuild 31 May '22

31 May '22

External Email - Use Caution Sending the info to your email shortly. - R. On May 31, 2022, at 00:56, Wojciech Górecki <goorec83(a)gmail.com> wrote:        External Email - Use Caution        Hello I wanted to ask whether you can send me the pass code for VB image: FS_7_2_0_ubuntu_18_04_06.ova.7z RegardsW. Górecki_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_surf2surf error: No such file or directory (but file exists)
by Salma Salhi 31 May '22

31 May '22

External Email - Use Caution Hello FreeSurfer Developers, I am trying to run the mri_surf2surf command as shown in this MRtrix tutorial on page 35 (https://secure-web.cisco.com/1IRfOd9DbtoZ73ePUy1kNxDjehQaayodvb_Pq3LttY1M2Y…) in order to map the annotation files of the HCP MMP 1.0 atlas. I keep running into a “No such file or directory” error when the code tries to read the “lh.orig” file, but the file is clearly in the required directory. Below is the output of my code: (base) salmasalhi@SalmasMacbookAir 100307_F26-30 % mri_surf2surf --srcsubject fsaverage --trgsubject subject_100307 --hemi lh --sval-annot $SUBJECTS_DIR/fsaverage/label/lh.glasser.annot --tval $SUBJECTS_DIR/subject_100307/label/lh.hcpmmp1.annot Setting mapmethod to nnf 7.2.0 setenv SUBJECTS_DIR /Users/salmasalhi/my_code/HumanBrain_v2/reconall cd /Users/salmasalhi/my_code/HumanBrain_v2/100307_F26-30 mri_surf2surf --srcsubject fsaverage --trgsubject subject_100307 --hemi lh --sval-annot /Users/salmasalhi/my_code/HumanBrain_v2/reconall/fsaverage/label/lh.glasser.annot --tval /Users/salmasalhi/my_code/HumanBrain_v2/reconall/subject_100307/label/lh.hcpmmp1.annot sysname Darwin hostname SalmasMacbookAir.local machine x86_64 user salmasalhi srcsubject = fsaverage srcval = (null) srctype = trgsubject = subject_100307 trgval = /Users/salmasalhi/my_code/HumanBrain_v2/reconall/subject_100307/label/lh.hcpmmp1.annot trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Users/salmasalhi/my_code/HumanBrain_v2/reconall/fsaverage/surf/lh.sphere.reg Loading source data Reading surface file /Users/salmasalhi/my_code/HumanBrain_v2/reconall/fsaverage/surf/lh.orig error: No such file or directory error: could not read annot file /Users/salmasalhi/my_code/HumanBrain_v2/reconall/fsaverage/label/lh.glasser.annot If I cd into the surf directory and check the files, this is the output: (base) salmasalhi@SalmasMacbookAir surf % ls lh.area lh.sphere.reg rh.inflated_avg lh.avg_curv lh.sphere.reg.avg rh.inflated_pre lh.avg_sulc lh.sulc rh.orig lh.avg_thickness lh.thickness rh.orig.avg.area.mgh lh.cortex.patch.3d lh.white rh.orig_avg lh.cortex.patch.flat lh.white.avg.area.mgh rh.pial lh.curv lh.white_avg rh.pial.avg.area.mgh lh.fsaverage_sym.sphere.reg lh.white_avg.H rh.pial_avg lh.inflated lh.white_avg.K rh.pial_semi_inflated lh.inflated.H mris_preproc.surface.lh.log rh.smoothwm lh.inflated.K mris_preproc.surface.rh.log rh.sphere lh.inflated_avg rh.area rh.sphere.reg lh.inflated_pre rh.avg_curv rh.sphere.reg.avg lh.orig rh.avg_sulc rh.sulc lh.orig.avg.area.mgh rh.avg_thickness rh.thickness lh.orig_avg rh.cortex.patch.3d rh.white lh.pial rh.cortex.patch.flat rh.white.avg.area.mgh lh.pial.avg.area.mgh rh.curv rh.white_avg lh.pial_avg rh.fsaverage_sym.sphere.reg rh.white_avg.H lh.pial_semi_inflated rh.inflated rh.white_avg.K lh.smoothwm rh.inflated.H lh.sphere rh.inflated.K (base) salmasalhi@SalmasMacbookAir surf % pwd /Users/salmasalhi/my_code/HumanBrain_v2/reconall/fsaverage/surf The “lh.orig” file is clearly in the right place. I tried to check the format of the file by typing mri_info lh.orig but the output was “ERROR: could not determine type of lh.orig”. Below are more details about my setup: 1) FreeSurfer version: freesurfer-darwin-macOS-7.2.0 2) Platform: macOS Monterey 12.3.1 (M1 chip) Thank you very much for your help, I greatly appreciate it. Salma Salhi

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Password for 7.2.0 VM box virtual machine
by niels.foit＠gmx.de 31 May '22

31 May '22

Dear all I require the password to unzip the above named archive. Since at least 10 people have asked this in the past hours, You might wanna reconsider the necessity of a password. Cheers niels External Email - Use Caution

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load PET.reg.lta freesurfer corregistration file in 3D slicer 4.11
by Gonzalo Rojas Costa 31 May '22

31 May '22

External Email - Use Caution Hi: I coregistered a PET file to a freesurfer data using mri_coreg command. I imported the freesurfer-generated data to 3D Slicer. How can I import the PET.reg.lta file in 3D Slicer? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 https://secure-web.cisco.com/1e17f0KeEx1uku6w91Y5lIGB5srmBKu9TQ3WRtpCV4CmGc… https://secure-web.cisco.com/1cs2LDGSTCr6GnV5Rq-K7aFHHjdJcgniT_IPajEDX9qitb… https://secure-web.cisco.com/1c3Ub-NigVjcMlUsRtymIbNmw_2reyZp6e5kdQWcxIjWpR… http://secure-web.cisco.com/1ptxxoRnoGXKniE15hzEh72mpWXmTkdcqzTdZL3sLc-LQjZ… https://secure-web.cisco.com/1V3s1u1ecjyempv27N_dkVM0NX2R9IvzTwxF-bXTbBaHXD…

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mris_flatten distortions
by Alberto Pisoni 31 May '22

31 May '22

External Email - Use Caution Hi all, I am trying to flatten a whole hemisphere, and i created the cut patch following the tutorials. see the result here. https://secure-web.cisco.com/1xjf27LYk5Ie25CTk51Q3cPiwVe-uMjYXB4V0ViZqlanRh… Then I run the command mris_flatten <input patch> <output patch> from the surf dir and it works, but when I visualize the patch it is distorted, like if I did not cut the inflated surface. https://secure-web.cisco.com/128ktBKDV9wlBus-Bu1XsphHIMQpHtnuoTRQ6748JzsrgK… What am I missing? The Freesurfer version is 7.2.0 (although I also tried with 6.0) and the system is a OS 11.6.1 BigSur Macbook Pro with M1 chip. Thanks Alberto ------------------------------------------------------ Alberto Pisoni, PhD Associate Professor Department of Psychology University of Milano-Bicocca Building U6 ~ Room 3139 piazza dell'Ateneo Nuovo 1 20126, Milano, Italy

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