Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

LGI failure
by Lena Palaniyappan 28 Dec '10

28 Dec '10

Hi Marie/ list Happy Christmas/New Year!! Any idea why this is happening while I try to recon-all for localGI? Error in ==> compute_lgi at 67 FacesInPialROI = [FacesInPialROI, mesh_total.facesOfVertex(j).faceList]; EDU>> ERROR: compute_lgi did not create output file '/Volumes/FREECOM/Applications/freesurfer/subjects/conn/conn02/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'! Darwin pmc10113.nottingham.ac.uk 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 recon-all -s conn02 exited with ERRORS at Sat Dec 25 09:23:23 GMT 2010 Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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pial surface in v5.0
by Lena Palaniyappan 28 Dec '10

28 Dec '10

I am not able to run recon-all localGI in v5.0 and I suspect this has something to do with the way pial surfaces are produced in v5.0 (the mris_make_surfaces bug) ERROR: compute_lgi did not create output file '/Volumes/FREECOM/Applications/freesurfer/subjects/conn/conn02/surf/tmp-mris_compute_lgi-lh.pial/lh.pial_lgi.asc'! Darwin pmc10113.nottingham.ac.uk 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 Is there any workaround/patching? Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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bad output of autorecon2 - is there any way to adjust it?
by Paola Valsasina 28 Dec '10

28 Dec '10

Dear Freesurfer experts, I have tried to analyze with Freesurfer a dataset of images acquired with a 3D T1 sequence without inversion pulse (unfortunately, it is simply a FFE sequence and not a MP-RAGE). Contrast between grey and white matter is not optimal in this image, and when I run -autorecon2 step I obtain a very bad output (attached). "white/grey" surface seems to be where the pial surface is expected to be, and pial surface is in the middle of csf. In your opinion, is it possible to obtain meaningful results with these images or not? Is there any setting of post-processing that I can change in order to obtain better surfaces? Thank you for any suggestion Kind regards, Paola ----------------------------------------------------------------------------------- SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. NON C'E' CURA SENZA RICERCA. Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele. Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org

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Paper amigdala volume
by Pedro Paulo de Magalhães Oliveira Junior 27 Dec '10

27 Dec '10

http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.2724.html http://www.nature.com/neuro/journal/vaop/ncurrent/extref/nn.2724-S1.pdf This paper made the first page in some major newspapers in Brazil today, and it uses FreeSurfer Cheers PPJ Enviado via iPad

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problems of Virtualtoolbox-Freesurfer
by Liukarl 27 Dec '10

27 Dec '10

Hello, Freesurfer users: I am new to Freesurfer. I have two questions when I tried to install the Virtualtoolbox-Freesurfer into Window-XP system. 1) I downloaded the VirtualBox 4.0 for Windows hosts, but in the step of “Adding the downloaded hard disk image”, there is no “Add” button that I can use add the disk image. Any idea how to fix this? 2) Say, eventually I successfully installed it. I have some other data from another Mac that I need to transfer to this windows computer. What folder I should put in my data that comply with the default SUBJECTS_DIR for further analysis? Thanks a lot! Karl

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missed label in cortical parcellation
by Anh Tuan 26 Dec '10

26 Dec '10

Dear Freesurfer users, After cortical parcellation, somehow the precentral and postcentral areas are mixed up and I'm not sure what could have caused this. Attached is a snap shot for your reference. Appreciate any hint given. Thanks Anthony

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Re: [Freesurfer] volume - surface shift in tkmedit
by Micheli, C. 25 Dec '10

25 Dec '10

Dear Bruce thank you for the quick answer. I saved the vox2ras matrix by assigning to it the voxel to millimiters transformation matrix the nifti converter read from dicom data (Siemens Magnetom Trio, 3T, sequence: standard mprage T1 't1_mprage_sag_std'). The tessellated mesh is saved in the millimiters space too (which means i applied the homogeneous transformation of voxel coordinates into millimiters) and in the millimiters space the volume and the mesh coincide. Actually the volume has been acquired as a 256X256X192 cube, and this could also cause a problem. I know realize that the volume has to be saved in RAS convention in order to be read in FreeSurfer correctly, about which i did not bother enough because the original voxel to nifti conversion matrix seems to have positioned the volume already in a convenient position. This is at least what i see when i visualized the so saved volume with tkmedit (coronal/sagittal/etc. are correctly positioned). Is everything clear about what i did? I though that since the two coordinate systems are the same they could be handled similarly in FS. How should i act on the surface in order to align it to the volume? If i would apply a topology fix on the mesh i will need the information about the white matter too, also saved in the same nifti format. In order to use this routine, do i also have to convert the volume in the proper RAS format or is it sufficient that volume and surface coincide in tkmedit visualization? (that was my intuitive criterion). About Freesurfer documentation that is what i found so far: http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?highlight=%28vox… Do you have other suggestions? There is a disclaimer on the documentation wiki. Sorry for the long email and i hope to hear from you soon. Happy Christmas! Cristiano ----- "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> schreef: > Van: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> > Aan: "C. Micheli" <c.micheli(a)fcdonders.ru.nl> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Verzonden: Woensdag 22 december 2010 15:26:37 > Onderwerp: Re: [Freesurfer] volume - surface shift in tkmedit > > Where did you get the vox2ras matrix that save_mgh takes? And what > space are the surface fiords in? There is extensive documentation on > our wiki fir the various coordinate systems we use > Cheers > Bruce > > > > On Dec 21, 2010, at 8:06 PM, "Micheli, C." <c.micheli(a)fcdonders.ru.nl> > wrote: > > > Dear all > > I would like to write an MRI anatomical volume and a surface in > freesurfer format. > > The surface is correspondent to the white matter tessellation, while > the volume represents T1 anatomical slices, both obtained from > softwares external to FreeSurfer. > > > > Using the two functions save_mgh.m and write_surf.m from the > freesurfer matlab interface files I am able to write the variables in > the proper freesurfer folders. > > > > In the original nifti format volume and surface match both in voxel > space and in millimiters space, but as soon as i visualize them in > tkmedit the surface is shifted. Any clue why this happens? Is there > any matrix that automatically translates the surface coordinates when > it is read in tkmedit? > > > > I hope to get your feedback soon > > > > Best regards > > Cristiano > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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.

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converting cortical thickness maps to NIFTI files
by Gallen, Courtney (NIH/NIDA) [F] 24 Dec '10

24 Dec '10

Hello, I'm interested in converting my cortical thickness maps to NIFTI files. Can you give me more information about how to do so? Also, is it possible to analyze freesurfer cortical thickness maps in AFNI (this is why I'm asking the question re conversion to NIFTI)? It seems as though my model is too complex to use something like qdec or fsgd (a 2x3 ANOVA with 3 covariates-1 discrete and 2 continuous). I see that I can specify my own design matrix to analyze the data with this model...but then don't see any info on what such a matrix should look like or how to proceed after that. Any help on either of these topics would be greatly appreciated! Thanks in advance Courtney Gallen Courtney Gallen Post-baccalaureate IRTA Neuroimaging Research Branch National Institute on Drug Abuse (IRP) 251 Bayview Blvd Suite 200 Baltimore, MD 21224 Tel: (443) 740-2631

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mri_mark_temporal_lobe
by FIDEL ALFARO ALMAGRO 24 Dec '10

24 Dec '10

Happy holidays for those who celebrate it today, Hi. Is there any documentation on how to use mri_mark_temporal_lobe application and what is its output? I cannot find any. Thanks in advance.

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cortical thickness of a ROI
by angela.favaro＠unipd.it 23 Dec '10

23 Dec '10

Dear all, I would appreciate any help about this point. I have a ROI created after a group comparison using functional data. I would like to explore the cortical thickness of this ROI to understand if differences in connectivity are linked to volumetric/thickness differences. I followed the instructions found in Freesurfer tutorials ('cortical thickness of a volume-defined ROI'). However, in the point 4 of the procedure I am not able to change the --reshape default. My run is: mri_surf2surf --s subj001 --trgsubject fsaverage --hemi rh --sval rh.thickness --tval rh.thickness.fsaverage.mgh --reshape-factor 7 but it continues to create (like default) a reshape with 6. For this reason, I think, the following command: mri_segstats --seg $SUBJECTS_DIR/rh.fsaverage.mask21.mgh --in rh.thickness.fsaverage.mgh --sum segstats-mask21.txt give: ERROR: dimension mismatch between input volume and seg input 27307 1 6 seg 23406 1 7 What can I do to solve this problem? Thank you for your help! Angela

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