Freesurfer

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30131 discussions

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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RES: memory requirement...
by Pedro Paulo de Magalhaes Oliveira Jr 20 Jul '09

20 Jul '09

1GB is the lower limit. Sometimes it can run out of memory or slow down by the swap Enviado do meu celular Nokia -----Msg original----- De: Gonzalo Rojas Enviada: 20/07/2009 21:03:36 Para: freesurfer(a)nmr.mgh.harvard.edu Assunto: [Freesurfer] memory requirement... Hi: I installed Freesurfer v4.4.0 in a PC with 1 GB RAM... There will be any problem to run Freesurfer in that PC, or only it runs slow ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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memory requirement...
by Gonzalo Rojas 20 Jul '09

20 Jul '09

Hi: I installed Freesurfer v4.4.0 in a PC with 1 GB RAM... There will be any problem to run Freesurfer in that PC, or only it runs slow ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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ascii file
by Feng-Xian 20 Jul '09

20 Jul '09

Hi, I have two problems want to solve. First, I want to know what coordinates it is, when I type the following command. mris_convert -c lh.thickness lh.white lh.thickness.asc Is it Tal coordinate?? Second, if the asc file doesn't use Tal coordinate, what commands do I type to obtain ? Bcause I really want to get the thickness asc with Tal coordinate. Thank you in advance! Feng-Xian ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)

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writing thickness of ROI to tabel (fwd)
by Bruce Fischl 18 Jul '09

18 Jul '09

---------- Forwarded message ---------- Date: Sat, 18 Jul 2009 13:44:22 +0200 From: Rosa Steimke <rosasteimke(a)gmx.de> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: writing thickness of ROI to tabel Hi freesurfer experts, iam trying to get the thichness of a Roi i specified in qdec into a table. i used the mris_anatmical stats command to generate stats for this roi for all participants. I tried the aparc2tabel command with different flags, but the roi i specified was never inside the table. wish flag do i have to use to get the roi that i drew in qdec? thanks in advance! rosa -------- Original-Nachricht -------- > Datum: Fri, 17 Jul 2009 14:35:55 -0400 (EDT) > Von: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > An: Rosa Steimke <rosasteimke(a)gmx.de> > CC: freesurfer(a)nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] mris_anatomical_stats > why is there a \ in your command line? > On Fri, 17 Jul 2009, Rosa Steimke > wrote: > >> >> Hi freesurfer experts, >> I have a problem using the mris_anatomical_stats command to generate > stats for a region of interest that i drew in qdec. >> It gives me the following error: >> >> >> >> >> [admins-imac:~/Rosa_MRTs] steimke% mris_anatomical_stats -l > rh.FUSIFORM.label \ -t rh.thickness -b -f 1/stats/rh.FUSIFORM.label 1 rh >> limiting computations to label rh.FUSIFORM.label. >> >> Flagged-options must go first in argument list. >> >> usage: mris_anatomical_stats [options] <subject name> <hemi> [<surface > name>] >> >> This program measures a variety of anatomical properties. >> >> Valid options are: >> >> -i <low thresh> <hi thresh> - only consider thicknesses in >> the specified range >> -l <.label file> - limit calculations to specified label >> -t <thickness file> - use specified file for computing >> thickness statistics >> -a <.annot file> - compute properties for each label >> in the annotation file separately >> -b - tabular output >> -f <tablefile> - table output to a file named tablefile >> (different format than -b) must specify >> an annotation file with -a or label >> file with -l >> -log <log> - will write the stats into a file >> named <log> >> -nsmooth <#> - will smooth the thicknessmap # of >> iterations before using it >> -c <.ctab file> - output the colortable for this annotation >> [admins-imac:~/Rosa_MRTs] steimke% mris_anatomical_stats -l > rh.FUSIFORM.label \ -t rh.thickness -b -f 1/stats/rh.FUSIFORM.label 1 rh >> >> >> >> >> do you know what i did wrong? >> thanks in advance! >> rosa >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01

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mris_anatomical_stats
by Rosa Steimke 17 Jul '09

17 Jul '09

Hi freesurfer experts, I have a problem using the mris_anatomical_stats command to generate stats for a region of interest that i drew in qdec. It gives me the following error: [admins-imac:~/Rosa_MRTs] steimke% mris_anatomical_stats -l rh.FUSIFORM.label \ -t rh.thickness -b -f 1/stats/rh.FUSIFORM.label 1 rh limiting computations to label rh.FUSIFORM.label. Flagged-options must go first in argument list. usage: mris_anatomical_stats [options] <subject name> <hemi> [<surface name>] This program measures a variety of anatomical properties. Valid options are: -i <low thresh> <hi thresh> - only consider thicknesses in the specified range -l <.label file> - limit calculations to specified label -t <thickness file> - use specified file for computing thickness statistics -a <.annot file> - compute properties for each label in the annotation file separately -b - tabular output -f <tablefile> - table output to a file named tablefile (different format than -b) must specify an annotation file with -a or label file with -l -log <log> - will write the stats into a file named <log> -nsmooth <#> - will smooth the thicknessmap # of iterations before using it -c <.ctab file> - output the colortable for this annotation [admins-imac:~/Rosa_MRTs] steimke% mris_anatomical_stats -l rh.FUSIFORM.label \ -t rh.thickness -b -f 1/stats/rh.FUSIFORM.label 1 rh do you know what i did wrong? 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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ANOVA and co-variable
by Zhang, Xiaochu (NIH/NIDA) [F] 17 Jul '09

17 Jul '09

Hi Freesurfer experts, I want to do a group ANOVA analysis with one co-variable. I have read the corresponding wiki but still have some problems. I need your help. I have 4 group subjects (A1B1, A1B2, A2B1, A2B2) and one co-vaiable (C). I want to get the interaction between A and B. However, because C is different in different groups, I need to rule out the influence from C in my ANOVA analysis. So the model is A*B+C. The fsgd file is GroupDescriptorFile 1 Title SK-SZ Class A1B1 Class A1B2 Class A2B1 Class A2B2 Variable C Input S1 A1B1 0.0 Input S2 A1B2 2.0 Input S3 A2B1 3.0 Input S4 A2B2 0.0 The mtx file is 0.5 -0.5 -0.5 0.5 0 0 0 0 Is it correct? Thanks a lot! Xiaochu Zhang PhD Visiting Research Fellow Neuroimaging Research Branch National Institute on Drug Abuse - IRP Biomedical Research Center 251 Bayview Blvd. Suite 200 (NIDA) Baltimore MD 21224 Tel: 443-740-2619

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