Re: [Freesurfer] FreeSurfer: fornix_and_versions
Bruce Fischl wrote: > Hi Judit, > > all the edits will be kept, so that shouldn't be a problem. It's hard > to diagnose the wm segmentation without looking at a volume, but if > they are really hyperintense you may need to manually fill them in in > the wm.mgz. As for mri_cc, you should use aseg.auto_noCCseg.mgz > instead of aseg.mgz via: > > mri_cc -aseg auto_noCCseg ... > > what is PLIC? The fornix should be non-zero after running this command. > > cheers, > Bruce > > On Mon, 20 Jul 2009, Judit Haasz wrote: > >> Bruce Fischl wrote: >>> Hi Judit, >>> >>> the fornix is labeled in the aseg, not the parcellation, although >>> this is not the default). If you rerun mri_cc with the -fornix >>> option it will write a volume named mri/fornix.mgz with the fornix >>> in it. >>> >>> cheers, >>> Bruce >>> >>> On Wed, 1 Jul 2009, Judit Haasz wrote: >>> Hi, We are trying to extract certain regions from FreeSurfer segmentation. There are couple of regions which are not found in the output files. We are currently searching for the regions in 13 output files. The regions are the following: right fornix (508), left fornix (558), right PLIC (158), left PLIC (157) and the starting, way and end points for cingulum and CST. Could you let us know in which file would we be able to find these regions? Is it possible that some regions are empty? Thank you for your help Judit Haasz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> Hi Bruce and all, >> >> >> I tried using the command as you suggested, but i get the following >> message: >> >> mri_cc -fornix STROKE_3T including fornix in segmentation >> reading aseg from >> /Applications/freesurfer//subjects/STROKE_3T/mri/aseg.mgz >> mri_cc: volume >> /Applications/freesurfer//subjects/STROKE_3T/mri/aseg.mgz already has >> CC in it >> >> Apart from that I encountered two more problems. >> Our subject group consists of 115 healthy elderly people. Some of the >> subjects` scan exhibit intensified white matter lesion which results >> in inaccurate pial surface reconstruction, that is pial surface >> penentrates into the white matter. Is there any way we could overcome >> this problem and obtain a more reliable segmentation? >> My next question refers to the problem of different FreeSurfer >> versions. We have data from 2005 and 2009. The ones from 2005 were >> processed by FreeSurfer ver 3.01. Now we are using FreeSurfer 4.3.0 >> with a separate mri_normalize program, that we received from you >> since a systematic error in the segmentation process was present. We >> are planning to compare the two datasets. We are aware of the fact >> that we have to rerun all subjects from 2005 with the version we are >> currently using. I am just wondering if there is a way to keep our >> previous wm and pial surface edits. As far as i know, edits can be >> kept if FreeSurfer is run from autorecon2. Would it be an option for >> us even though, mri_normalize is involved in autorecon1. >> >> I really appreciate your help >> >> Judit Haasz >> >> >> >> >> Hi, mri_cc -fornix works now. Is it possible to segment any other white matter pathway or tracking point that are not in the default, but appear in FreeSurferColorLut? Considering pial surface reconstruction, what can i do if the pial surface penentrates into the cortical GM, not following the brain surface? How shall I proceed with re-running subjects from 2005? How would all of our edits be kept? Thanks, Judit ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Fwd:autorecon2-error
Hello,freesurfer experts I test freesurfer on my computer and run"recon-all -s bert -autorecon1" and "recon-all -s bert -autorecon3" successfully, but run "recon-all -s bert -autorecon2",there were some errors,as follows: . > > # > > #...@# Cortical ribbon mask Mon Jul 13 02:59:19 CST 2009 > > /home/whb/soft/freesurfer/subjects/bert/mri > > > > mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance bert mris_volmask.bin: error while loading shared libraries: /home/whb/soft/freesurfer/lib/vtk/lib/vtk-5.2/libvtkRendering.so.5.2: cannot restore segment prot after reloc: Permission denied Linux localhost.localdomain 2.6.21-1.3194.fc7 #1 SMP Wed May 23 22:35:01 EDT 2007i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Mon Jul 13 02:59:20 CST 2009 when I run Qdec, it also showed "libvtkRendering.so.5.2" error.I don't know what's the reason. would you like to help me£¿ Thanks in advance. Hai-bao Wang Jul-21, 2009 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] freesurfer's template for sphere registration
Hi Freesurfer experts, I asked this question previously, but I found it problematic when displayed in your mailist. I'm sorry that the question still not solved and I feel sorry to trouble you again. In your sphere registration in freesurfer, the procedure is like: creating the template.tif by mris_make_template. The template you use in Freesurferis created by iterative registration of 40 subjects, according to "High-resolution inter-subject averaging and a coordinate system for the cortical surface, Fischl, B., Sereno, M.I., Tootell, R.B.H., and Dale, A.M., (1999). Human Brain Mapping, 8:272-284(1999)". So, after the template generation process, you will get a .tif file which include the necessary infomation (like the means and variances of curv, sul from the aligned spheres). But,do you have the other information of this final template, such as the sphere representation, folded surface representation of this template? I know that under */subjects/fsaverage/surf, there are some surface representations of the average of the 40 subjects, but to my knowledge, they are just used for visulazation and are not the surface representation of the template.tif you used, am I right? 2, subjects' sphere registration to the template sphere In this process, we can get the deformed subjects spheres( *.reg ), which have a one-to-one correspondance to the original subject surfaces. Except the .reg sphere with the cuvature information, do you have any other form of representation of the deformed sphere? You know that there are other kinds of surface mapping methods, like Miller's Large Defformation deffeomrphic surface mapping, they just do surface mapping using the folded surfaces. After surface mapping, they will get the deformed folded surface which would be aligned with the template folded surface. With the deformed subject and template folded surfaces, they can tell directly which sulcus or gyrus is aligned well. So, for your mapping, when I get the deformed sphere, do you have any command or method to put the sphere back to the folded surface so I can see the suci and gyri directly? If you also have the surface representation of the template, then i can superimpose them to see how good the alignment is. If you think I didn't state this problem clearly, please refer to an example in the following: I found one reference using your sphere registration method. "Simplified Intersubject Averaging on the Cortical Surface Using SUMA"Brenna D. Argall, Ziad S. Saad,and Michael S. Beauchamp"Human Brain Mapping 27:14 –27(2006)" You may see the attachment in : https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-May/010558.html In "Spherical Morphing" section, They mentioned that " Using the mris_register [Fischl et al., 1999b] routine, each individual subject’s surface was registered to the FreeSurfer average7 template prior to node number standardization. Standardization and averaging were then performed on the surfaces as described above" (using SUMA FYI). From this part, I assume that all the deformed surfaces are in spherical representation. Then in the result part, in section "Intersubject Averaging of Functional Data: Different Surface Methods", they mentioned they " in order to compare the AC–PC method to these more complex algorithms, the FreeSurfer program mris_register [used in Fischl et al., 1999b] was used to morph the cortical surface models to a predefined template, and these morphed surface models were then used to create a morphed surface average." In Fig7C ：Average surface created by averaging the same 28 subjects using mris_register standardization. You can see that they show the average surface in a folded surface representation, not a sphere. Could you give me a hint that how they do this since you only have a sphere representation of the aligned surface? -- Regards, Jidan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FreeSurfer: fornix_and_versions
Hi Judit, there is a white matter parcellation that is run by default called wmparc.mgz. Anything else is future work. The pial surface misplacement is usually a result of the white matter being wrong, but the intervention depends on the problem, so we'd need to see the example. As for the edits, they should be kept when you rerun -all. cheers, Bruce On Tue, 21 Jul 2009, Judit Haasz wrote: > Bruce Fischl wrote: >> Hi Judit, >> >> all the edits will be kept, so that shouldn't be a problem. It's hard to >> diagnose the wm segmentation without looking at a volume, but if they are >> really hyperintense you may need to manually fill them in in the wm.mgz. As >> for mri_cc, you should use aseg.auto_noCCseg.mgz instead of aseg.mgz via: >> >> mri_cc -aseg auto_noCCseg ... >> >> what is PLIC? The fornix should be non-zero after running this command. >> >> cheers, >> Bruce >> >> On Mon, 20 Jul 2009, Judit Haasz wrote: >> >>> Bruce Fischl wrote: Hi Judit, the fornix is labeled in the aseg, not the parcellation, although this is not the default). If you rerun mri_cc with the -fornix option it will write a volume named mri/fornix.mgz with the fornix in it. cheers, Bruce On Wed, 1 Jul 2009, Judit Haasz wrote: > Hi, > > We are trying to extract certain regions from FreeSurfer segmentation. > There are couple of regions which are not found in the output files. We > are currently searching for the regions in 13 output files. > The regions are the following: right fornix (508), left fornix (558), > right PLIC (158), left PLIC (157) and the starting, way and end points > for cingulum and CST. > > Could you let us know in which file would we be able to find these > regions? Is it possible that some regions are empty? > > Thank you for your help > > Judit Haasz > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >>> Hi Bruce and all, >>> >>> >>> I tried using the command as you suggested, but i get the following >>> message: >>> >>> mri_cc -fornix STROKE_3T including fornix in segmentation >>> reading aseg from >>> /Applications/freesurfer//subjects/STROKE_3T/mri/aseg.mgz >>> mri_cc: volume /Applications/freesurfer//subjects/STROKE_3T/mri/aseg.mgz >>> already has CC in it >>> >>> Apart from that I encountered two more problems. >>> Our subject group consists of 115 healthy elderly people. Some of the >>> subjects` scan exhibit intensified white matter lesion which results in >>> inaccurate pial surface reconstruction, that is pial surface penentrates >>> into the white matter. Is there any way we could overcome this problem and >>> obtain a more reliable segmentation? >>> My next question refers to the problem of different FreeSurfer versions. >>> We have data from 2005 and 2009. The ones from 2005 were processed by >>> FreeSurfer ver 3.01. Now we are using FreeSurfer 4.3.0 with a separate >>> mri_normalize program, that we received from you since a systematic error >>> in the segmentation process was present. We are planning to compare the >>> two datasets. We are aware of the fact that we have to rerun all subjects >>> from 2005 with the version we are currently using. I am just wondering if >>> there is a way to keep our previous wm and pial surface edits. As far as i >>> know, edits can be kept if FreeSurfer is run from autorecon2. Would it be >>> an option for us even though, mri_normalize is involved in autorecon1. >>> >>> I really appreciate your help >>> >>> Judit Haasz >>> >>> >>> >>> >>> > Hi, > > mri_cc -fornix works now. Is it possible to segment any other white matter > pathway or tracking point that are not in the default, but appear in > FreeSurferColorLut? > Considering pial surface reconstruction, what can i do if the pial surface > penentrates into the cortical GM, not following the brain surface? > How shall I proceed with re-running subjects from 2005? How would all of our > edits be kept? > > Thanks, > Judit > > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] freesurfer's template for sphere registration
Hi Jidan, the atlas only exists in spherical coords. To represent a folded surface we either (1) map to an individual subject, or (2) use a volume transform such as tal and the vertex correspondence from the sphere.reg to find the average coordinate of a vertex. This is how we build the fsaverage and average7 surfaces (we know this is a hack, but it's easy and a good visualization tool). You can use the mapping to paint the geometry of one subject onto another folded surface if you want to visualize the geometric mapping (e.g. the curv of one subject on the white surface of another). cheers, Bruce On Tue, 21 Jul 2009, Zhong Jidan wrote: Hi Freesurfer experts, I asked this question previously, but I found it problematic when displayed in your mailist. I'm sorry that the question still not solved and I feel sorry to trouble you again. In your sphere registration in freesurfer, the procedure is like: creating the template.tif by mris_make_template. The template you use in Freesurferis created by iterative registration of 40 subjects, according to "High-resolution inter-subject averaging and a coordinate system for the cortical surface, Fischl, B., Sereno, M.I., Tootell, R.B.H., and Dale, A.M., (1999). Human Brain Mapping, 8:272-284(1999)". So, after the template generation process, you will get a .tif file which include the necessary infomation (like the means and variances of curv, sul from the aligned spheres). But,do you have the other information of this final template, such as the sphere representation, folded surface representation of this template? I know that under */subjects/fsaverage/surf, there are some surface representations of the average of the 40 subjects, but to my knowledge, they are just used for visulazation and are not the surface representation of the template.tif you used, am I right? 2, subjects' sphere registration to the template sphere In this process, we can get the deformed subjects spheres( *.reg ), which have a one-to-one correspondance to the original subject surfaces. Except the .reg sphere with the cuvature information, do you have any other form of representation of the deformed sphere? You know that there are other kinds of surface mapping methods, like Miller's Large Defformation deffeomrphic surface mapping, they just do surface mapping using the folded surfaces. After surface mapping, they will get the deformed folded surface which would be aligned with the template folded surface. With the deformed subject and template folded surfaces, they can tell directly which sulcus or gyrus is aligned well. So, for your mapping, when I get the deformed sphere, do you have any command or method to put the sphere back to the folded surface so I can see the suci and gyri directly? If you also have the surface representation of the template, then i can superimpose them to see how good the alignment is. If you think I didn't state this problem clearly, please refer to an example in the following: I found one reference using your sphere registration method. "Simpliÿÿed Intersubject Averaging on the Cortical Surface Using SUMA"Brenna D. Argall, Ziad S. Saad,and Michael S. Beauchamp"Human Brain Mapping 27:14 ÿÿ27(2006)" You may see the attachment in : https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-May/010558.html In "Spherical Morphing" section, They mentioned that " Using the mris_register [Fischl et al., 1999b] routine, each individual subjectÿÿs surface was registered to the FreeSurfer average7 template prior to node number standardization. Standardization and averaging were then performed on the surfaces as described above" (using SUMA FYI). From this part, I assume that all the deformed surfaces are in spherical representation. Then in the result part, in section "Intersubject Averaging of Functional Data: Different Surface Methods", they mentioned they " in order to compare the ACÿÿPC method to these more complex algorithms, the FreeSurfer program mris_register [used in Fischl et al., 1999b] was used to morph the cortical surface models to a predeÿÿned template, and these morphed surface models were then used to create a morphed surface average." In Fig7C ÿÿAverage surface created by averaging the same 28 subjects using mris_register standardization. You can see that they show the average surface in a folded surface representation, not a sphere. Could you give me a hint that how they do this since you only have a sphere representation of the aligned surface? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Estimated total incranial volume
Dear All, In addition to eTIV based on Tailarach transform matrix (see Buckner et al. paper), is there other estimated total intracranial volume method, for example, using the BET2 (brain extraction tool)? Thank you in advance, Flavio ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
