Freesurfer July 2009

freesurfer@nmr.mgh.harvard.edu

85 participants
135 discussions

WM bug fix
by Tricia Merkley 23 Jul '09

23 Jul '09

Hi, I tried to use the white matter bug fix using v4.4.0 for data that was originally run using v4.0.4. I then noticed that the IntraCranialVol measure in wmparc.stats and aseg.stats for one of the subjects was -2083.23 (after rerunning recon-all -segstats -wmparc). Is this due to the new way of calculating TIV (as of v4.3.0)? Should I revert back to using the values prior to the bug fix? Here is the bugr info if needed: FREESURFER_HOME: /fslhome/mendy22/freesurfer4.4.0 Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.4.0 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-53.1.14.el5 x86_64 cmd line executed: recon-all -s <subject_id> -segstats -wmparc Thanks so much, Tricia Merkley

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recon-all exited with errors
by sameer kumar 22 Jul '09

22 Jul '09

hi all, I ran recon-all on a case, and it exited with errors, and the error message looks like this: ERROR: Talairach QA check failed! z-score = -6 <= -6 = threshold Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. will there be a difference in the results if i use that flag to skip the test? Thanks, Regards, Sameer

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left right nifti
by Narly A Golestani 22 Jul '09

22 Jul '09

Hello everyone, I would like to know if there are left-right orientation issues when converting images from nifti format to the mgz format. I suspect not as nifti, unlike analyze, contains the left-right information in the file itself. But I would like to make sure that there are not issues such as the ones reported with going through analyze, such those reported here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg09329.html thanks in advance! best wishes, Narly.

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Estimated total incranial volume
by Flavio Seixas 22 Jul '09

22 Jul '09

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

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Colortable
by Eylem Kirlangic 22 Jul '09

22 Jul '09

Hi, Is there any way to extend the colortable in freesurfer? Cheers, Eylem ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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floating area with significant difference in qdec
by Rosa Steimke 22 Jul '09

22 Jul '09

dear freesurfer experts! I am trying to make a ROI of an area the showed significant difference in qdec. to do so i am drawing around the area per hand, but it doesnt look very precies. is there also a function that will float the whole area which is coloured? thanks in advance! rosa -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01

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skull-scalp volume extraction
by Tommaso De Marco 22 Jul '09

22 Jul '09

Hi all, I have to implement a Difference element method on a volume extracted from a mri. Using freesurfer I am able to extract the volume file for the brain (ie. $h.ribbon), but I need also the volume files for the skull and for the skin. I have seen that the flag -surf exits in the watershed command to extract only the superficial meshes of these. I have also tried to use the flag -LABEL; according to the manual the option -LABEL adds a label for each voxel according to the region in which it is located: 0 -> exterior 1 -> scalp 2 -> skull 3 -> csf 4 -> gray 5 -> white 6 -> fat tissue but the results are completely wrong, for example I have a label 3 also for regions external to the scalp! Could someone please help me explaining how to use the watershed command using the -LABEL option?

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freesurfer's template for sphere registration
by Zhong Jidan 21 Jul '09

21 Jul '09

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

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FreeSurfer: extracting regions from segmentation
by Judit Haasz 21 Jul '09

21 Jul '09

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

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Fwd:autorecon2-error
by whblqh＠mail.ustc.edu.cn 21 Jul '09

21 Jul '09

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

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Freesurfer July 2009