[Freesurfer] Transform a surface (e.g., lh.white) with a register.dat (12 dof)
External Email - Use Caution Hi FreeSurfer developer, I want to transform surfaces files (lh.white, lh.pial, rh.white, and rh.pial) with a registration matrix that has 12 degrees of freedom. Is there a function in FreeSurfer that can do so? Very best, Yixin Ma ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_surf2vol method one
External Email - Use Caution Hi Freesurfer experts, I'm trying to write the normals of the GM/WM meshes to the entire ribbon. We usually do it by: 1) Generate normal files from rh.white and lh.white mris_convert rh.white rh.white.gii mris_convert -n rh.white rh.white.normals.asc 2) Use matlab 'read_normals' function to read the normals and write individual directions xyz as a paint format file. g = gifti([path 'Analysis/' exam '/' subject '/surf/rh.white.gii']); norm = read_normals(g,[path 'Analysis/' exam '/' subject '/surf/rh.white.normals.asc']); write_wfile([path 'Analysis/' exam '/' subject '/surf/rh_normx.w' ],norm(:,1)); write_wfile([path 'Analysis/' exam '/' subject '/surf/rh_normy.w' ],norm(:,2)); write_wfile([path 'Analysis/' exam '/' subject '/surf/rh_normz.w' ],norm(:,3)); 3) Use mri_surf2vol method two to paint the normals into the ribbon. But the problem is that method two gives me lots of holes in the ribbon. I'm wondering if it's possible to use mri_surf2vol method one to paint the normals into the ribbon because method one does not leave holes in the ribbon. However, it seems like the overlay does not accept paint file format (rh_normx.w). The overlay in method one accepts rh.thickness as an input, as shown in the example on the website. I'm wondering how to convert the painting files to have the same format as rh.thickness? Thank you in advance, Yixin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Run FreeSurfer recon-all on isoDWI
External Email - Use Caution I was trying to use the average of DWI images (isoDWI) to run recon-all, and it didn't work. I understand that FreeSurfer can only take a T1-weighted image for now. But how hard would it be to modify the code by myself to make it work? If it works, how accurate do you think it would be to run FreeSurfer on isoDWI? All the best and thank you for your help, Yixin Message: 8 Date: Fri, 13 Mar 2020 18:44:18 -0400 From: "Douglas N. Greve" Subject: Re: [Freesurfer] FreeSurfer Cortical Parcellation using isoDWI image only? To: Message-ID: <14b89d9d-130f-08f0-d593-71f2cdef3...@mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" you are trying to run a DWI image through recon-all? Sorry, it can only take T1w right now On 3/12/2020 3:28 PM, Yixin Ma wrote: > > External Email - Use Caution > > Hi Freesurfer experts, > > I'm writing to ask if it's possible to run FreeSurfer Cortical > Parcellation by just using the isoDWI image. If it's possible, it will > reduce the scan time and avoid misregistration between T1 and DWI. > > I started from just input the masked isoDWI (mask generated from > MRtrix3) for -reconall command, and attached is a screenshot of the > image of NU.mgz, which shows a clear delineation of WM/GM matter. So I > think it's promising, although the recon-all stopped because of the > wrong contrast. > My ideas on tackling this problem are: > 1) generate a corresponding "fake" T1-weighted image by > either?adjusting the value directly or using a brain Atlas and > deformable registration to create one. > 2) Tweak some parameters in FreeSurfer. > > Any suggestions or comments on my ideas are appreciated. > > Thank you very much and all the best, > > Yixin Ma > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] hippocampus subfield division
External Email - Use Caution Hi Freesurfer experts, I'm writing to ask about the hippocampus subfield division again. Last time, I gave you an example of the subject that I failed to run the hippocampal subfield division, and you told me that you were able to run the hippocampus subfield on your laptop. I was using the older command of recon-all -all -s bert -hippocampal-subfields-T1. Should I try to use the newer version: segmentHA_T1.sh bert [SUBJECTS_DIR]. Is that possible FreeSurfer upgrading is the reason that I failed to run a subject on my server recently (but I was able to run it before). Also, can I ask where can I find the file of segmentHA_T1.sh? Thanks for your help. Cheers, Yixin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] DKT40 classifier atlas
External Email - Use Caution Hi Freesurfer experts, I'm writing to ask how can I reconstruct the DKT40 classifier atlas. Is it included in recon -all? Thank you for your help. Best regards, Yixin Ma ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampus subfield division error
External Email - Use Caution Hi Dr. 00246.zip <https://drive.google.com/file/d/17ZePu_X5BqpJNT2u5yEUhNHh8jH1dSIL/view?usp=drive_web> Iglesias I have the problem of hippocampus subfield division not working. You mentioned that I can upload one of the subjects as an example. I'm not sure what kinds of file do you want, so I uploaded the folder of the FreeSurfer reconstruction results, as attached. Thank you again for your help. Best regards, Yixin On Fri, Jan 18, 2019 at 12:28 PM Yixin Ma wrote: > Hi, > > The hippocampus subfields division problem happens on more than one > subjects (~10). However, I have successfully run it on one subject (which > is a little earlier in time, before I failed to run recent 10 subjects). > Thank you for your help. > > Best regards, > > Yixin > > -- Forwarded message - > From: Yixin Ma > Date: Fri, Jan 18, 2019 at 11:04 AM > Subject: Hippocampus subfield division error > To: > > > Hi FreeSurfer experts, > > I'm writing to ask about the hippocampus subfields division in FreeSurfer > 6.0. > > I got an error message as attached, could you please help me with which > part might have gone wrong? This subject's other recon-all worked but not > for hippocampus subfields division. > > Thank you for your help. > > Best regards, > > Yixin > > [ > In segmentSubjectT1_autoEstimateAlveusML at 325] > Reading contexts of file > /usr/local/packages/freesurfer_v6.0.0/average/HippoSF/atlas/compressionLookupTable.txt > -- > Making Lateral-nucleus map to reduced label 1 > Making Paralaminar-nucleus map to reduced label 1 > Making Basal-nucleus map to reduced label 1 > Making Accessory-Basal-nucleus map to reduced label 1 > Making Corticoamygdaloid-transitio map to reduced label 1 > Making Central-nucleus map to reduced label 1 > Making Cortical-nucleus map to reduced label 1 > Making Medial-nucleus map to reduced label 1 > Making Anterior-amygdaloid-area-AAA map to reduced label 1 > -- > Making alveus map to reduced label 2 > Making Hippocampal_tail map to reduced label 2 > Making HATA map to reduced label 2 > Making fimbria map to reduced label 2 > Making parasubiculum map to reduced label 2 > Making hippocampal-fissure map to reduced label 2 > -- > Making Left-Cerebral-Cortex map to reduced label 3 > -- > Making Left-Cerebral-White-Matter map to reduced label 4 > -- > Making Left-Lateral-Ventricle map to reduced label 5 > -- > Making Left-choroid-plexus map to reduced label 6 > -- > Making Unknown map to reduced label 7 > -- > Making Left-VentralDC map to reduced label 8 > -- > Making Left-Putamen map to reduced label 9 > -- > Making Left-Pallidum map to reduced label 10 > -- > Making Left-Thalamus-Proper map to reduced label 11 > -- > Making Left-Accumbens-area map to reduced label 12 > -- > Making Left-Caudate map to reduced label 13 > Error using segmentSubjectT1_autoEstimateAlveusML (line 348) > The vector of prior probabilities in the mesh nodes must always sum to one > over all classes > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampus subfield division error
External Email - Use Caution Hi, The hippocampus subfields division problem happens on more than one subjects (~10). However, I have successfully run it on one subject (which is a little earlier in time, before I failed to run recent 10 subjects). Thank you for your help. Best regards, Yixin -- Forwarded message - From: Yixin Ma Date: Fri, Jan 18, 2019 at 11:04 AM Subject: Hippocampus subfield division error To: Hi FreeSurfer experts, I'm writing to ask about the hippocampus subfields division in FreeSurfer 6.0. I got an error message as attached, could you please help me with which part might have gone wrong? This subject's other recon-all worked but not for hippocampus subfields division. Thank you for your help. Best regards, Yixin [ > In segmentSubjectT1_autoEstimateAlveusML at 325] Reading contexts of file /usr/local/packages/freesurfer_v6.0.0/average/HippoSF/atlas/compressionLookupTable.txt -- Making Lateral-nucleus map to reduced label 1 Making Paralaminar-nucleus map to reduced label 1 Making Basal-nucleus map to reduced label 1 Making Accessory-Basal-nucleus map to reduced label 1 Making Corticoamygdaloid-transitio map to reduced label 1 Making Central-nucleus map to reduced label 1 Making Cortical-nucleus map to reduced label 1 Making Medial-nucleus map to reduced label 1 Making Anterior-amygdaloid-area-AAA map to reduced label 1 -- Making alveus map to reduced label 2 Making Hippocampal_tail map to reduced label 2 Making HATA map to reduced label 2 Making fimbria map to reduced label 2 Making parasubiculum map to reduced label 2 Making hippocampal-fissure map to reduced label 2 -- Making Left-Cerebral-Cortex map to reduced label 3 -- Making Left-Cerebral-White-Matter map to reduced label 4 -- Making Left-Lateral-Ventricle map to reduced label 5 -- Making Left-choroid-plexus map to reduced label 6 -- Making Unknown map to reduced label 7 -- Making Left-VentralDC map to reduced label 8 -- Making Left-Putamen map to reduced label 9 -- Making Left-Pallidum map to reduced label 10 -- Making Left-Thalamus-Proper map to reduced label 11 -- Making Left-Accumbens-area map to reduced label 12 -- Making Left-Caudate map to reduced label 13 Error using segmentSubjectT1_autoEstimateAlveusML (line 348) The vector of prior probabilities in the mesh nodes must always sum to one over all classes ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Hippocampus subfield division error
External Email - Use Caution Hi FreeSurfer experts, I'm writing to ask about the hippocampus subfields division in FreeSurfer 6.0. I got an error message as attached, could you please help me with which part might have gone wrong? This subject's other recon-all worked but not for hippocampus subfields division. Thank you for your help. Best regards, Yixin [ > In segmentSubjectT1_autoEstimateAlveusML at 325] Reading contexts of file /usr/local/packages/freesurfer_v6.0.0/average/HippoSF/atlas/compressionLookupTable.txt -- Making Lateral-nucleus map to reduced label 1 Making Paralaminar-nucleus map to reduced label 1 Making Basal-nucleus map to reduced label 1 Making Accessory-Basal-nucleus map to reduced label 1 Making Corticoamygdaloid-transitio map to reduced label 1 Making Central-nucleus map to reduced label 1 Making Cortical-nucleus map to reduced label 1 Making Medial-nucleus map to reduced label 1 Making Anterior-amygdaloid-area-AAA map to reduced label 1 -- Making alveus map to reduced label 2 Making Hippocampal_tail map to reduced label 2 Making HATA map to reduced label 2 Making fimbria map to reduced label 2 Making parasubiculum map to reduced label 2 Making hippocampal-fissure map to reduced label 2 -- Making Left-Cerebral-Cortex map to reduced label 3 -- Making Left-Cerebral-White-Matter map to reduced label 4 -- Making Left-Lateral-Ventricle map to reduced label 5 -- Making Left-choroid-plexus map to reduced label 6 -- Making Unknown map to reduced label 7 -- Making Left-VentralDC map to reduced label 8 -- Making Left-Putamen map to reduced label 9 -- Making Left-Pallidum map to reduced label 10 -- Making Left-Thalamus-Proper map to reduced label 11 -- Making Left-Accumbens-area map to reduced label 12 -- Making Left-Caudate map to reduced label 13 Error using segmentSubjectT1_autoEstimateAlveusML (line 348) The vector of prior probabilities in the mesh nodes must always sum to one over all classes ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Hippocampus cortical layers division
External Email - Use Caution Hi Freesurfer experts, I'm writing to ask if you have any suggestions on generating cortical layers for hippocampus subfield cortical regions with the help of freesurfer. When generating cortical layers for other neocortex brain region, the surface files for pial and white/gray matter interface surface are required. But we don't have that surface data for hippocampus subfield division. Is that possible that I can generate those files? Thank you for your help in advance. Yixin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] hippocampus cortex surface
External Email - Use Caution Hi Freesurfer experts, After running the segmentation of hippocampus subfields, I'm wondering if I can get the surface of the gray matter and white matter of hippocampus in addition to subfields. My goal is to divide the hippocampus cortex into multiple layers. Thanks for your help in advance. Yixin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] co-registration between slab of DTI image
External Email - Use Caution Hi Freesurfer experts, I'm writing to ask about coregistration between a thin oblique coronal slab of DTI image ( only 15 slices) and a cubic 1x1x1 voxel size anatomical image (volume size is 256x256x256), with additional whole brain low-resolution DTI to assist registration. The codes I use are as attached: I have few concerns: 1) the input oblique coronal slab of DWI image does not have header information, should it be better if I input the DWI slab in RAS coordinates (axial volume)? 2) Should I zero-fill the DWI slab to match the volume of T1.mgz? I already did that because it won't start to calculate the cost function between the thin DWI slab and anatomical image if I don't zero-fill. However, I feel like the cost function cannot make sense of the fact that the zeros are already outside the region of interest. 3) Should I use --init-fsl /--init-spm in this case? Neither of these two worked. Is there a better optimization function recommended? I have been using fsl flirt function 2 step registration (from DWI slab to whole brain DWI; From whole brain DWI to whole brain anatomical image) to do the registration. But I don't think it's the best way. For freesurfer bbregister, I have been trying to change things here and there, but the co-registration does not work well. Do you suggest to look at any parameter particularly based on this scenario? Thank you for your help, Yixin Note that isoDWI111_256_axial.nii is the slab of DWI image EPI_iso111_256_axial.nii is the whole brain DWI image [The freesurfer reconstruction is performed before all these] bbregister --s 30426 --mov isoDWI111_256_axial.nii --*int* EPI_iso111_256_axial.nii --init-fsl --reg xform_freesurfer.dat --dti tkregister2 --reg xform_freesurfer.dat --mov isoDWI111_axial.nii mri_vol2vol --reg xform_freesurfer.dat --mov isoDWI111_axial.nii --fstarg --o isoDWI111-*in*-anat.mgh mri_convert isoDWI111-*in*-anat.mgh isoDWI111_reg.nii ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Search angle limitation in the flirt registration
Hi freesurfer developers and users, I'm writing to ask about the search angle limitation (--searchrx, -- searchry and --searchrz) in the flirt function. I use the search angle option a lot for limited angle search, which usually generate a better registration result compared with the broad angle search. But I still don't quite understand how rx,ry and rz are defined and how negative and positive angles affect the result. Because sometimes I find the result after the angle limitation does not align well with my expectation of rotation angle. Thank you for your help, Yixin Ma Brain Image and Analysis Center Duke university ___ 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.
