Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Semi-Inflated Surfaces
by Liang, Kelvin 02 Nov '09

02 Nov '09

Hi FS Folks, I've often seen articles present their data on semi-inflated cortical surfaces, and I'd like to display my regions of interest in such a format. However, I've only found inflated, pial, and white surface options in qdec or tksurfer. Am I overlooking an option somewhere? Thank you for your assistance, Kelvin -- Kelvin Y. Liang MSTP, School of Medicine Washington University in St. Louis The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] Surface area of subcortical structures
by Elizabeth Selgrade 02 Nov '09

02 Nov '09

Hi Nick, Why do you use 128 as the value for mri_tessellate in your suggestion below? Should this value be used for all ROIs, regardless of hemisphere? Thank you, Liz Selgrade -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Wednesday, September 16, 2009 3:16 PM To: Douglas N Greve Cc: Elizabeth Selgrade; 'freesurfer(a)nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] Surface area of subcortical structures or use mri_extract_label instead of mri_binarize, like this, to get the left hippocampus: mri_extract_label aseg.mgz 17 lh.hippo.mgz mri_tessellate lh.hippo.mgz 128 lh.hippo.unsmoothed mris_smooth lh.hippo.unsmoothed lh.hippo mris_info lh.hippo |& grep total_area this seems to work. '17' is the index for left hippocampus, as found in $FREESURFER_HOME/FreeSurferColorLUT.txt Nick On Wed, 2009-09-16 at 15:05 -0400, Douglas N Greve wrote: > There's not an easy way. You could binarize the structure > (mri_binarize), then build a surface around it (mri_tessellate), maybe > smooth it (mris_smooth), then compute the surface area (mris_info). > This would be a completely untested method though:). > > Elizabeth Selgrade wrote: > > Hello, > > > > Is there a way to get the surface area of FreeSurfer subcortical structures? > > > > Thanks, > > Liz Selgrade > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > >

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Job announcement
by Derin Cobia 02 Nov '09

02 Nov '09

Posted on behalf of a colleague: FACULTY POSITION, MEG-fMRI NEUROIMAGING Saint Louis University, is a Jesuit, Catholic university dedicated to teaching, research, health care and community service and is seeking a scientist at an open rank level for a non-tenure track, grant-funded faculty position in the Division of Neurosurgery, Department of Surgery at St. Louis University School of Medicine. The successful candidate will head the Division’s imaging research using the installed 275 channel magnetoencephalography (MEG) system and 3 Tesla MRI and manage a multimillion dollar research grant funded by the Department of Defense. This project will span 4 years and study traumatic brain injury in combat veterans using MEG, positron emission tomography (PET/CT) and functional MRI with diffusion tensor imaging (fMRI with DTI). ). A team of research staff members has been assembled to perform the study assisted by graduate and post-graduate students assigned to the project. The ideal candidate would hold a Ph.D. in any of the following areas: biomedical engineering, physiology, experimental/cognitive psychology, neuroscience, MEG, or other applicable disciplines. Candidates should be familiar with standard computational software packages for neuro-imaging such as Curry, Unix, MatLab, Slicer, and C/C++, and have at least five (5) years of clinical research experience, preferably in the neurosciences. Previous experience in neurological functional imaging is expected. Preferred candidates will have proficiency in epidemiology, biostatistics, registration techniques using deformable templates to create standardized atlases, and training/certification in clinical research. Salary will be commensurate with academic credentials and experience. Candidates will be expected to apply and obtain funding from external agencies to continue the work of the Division within the area of neuroimaging using the installed base of equipment. Interested candidates should submit a cover letter, application, relevant reprints, and current curriculum vitae to http:// jobs.slu.edu. An initial letter of interest describing current research interests and future research goals should be sent along with a curriculum vitae to: Richard Bucholz, MD, FACS Director and Professor, Division of Neurosurgery Department of Surgery Saint Louis University 3635 Vista Ave. St. Louis, MO 63110-0250 Phone: 314-577-8795 Email: Richard(a)bucholz.org Saint Louis University is an affirmative action, equal opportunity employer, and encourages nominations and applications of women and minorities.

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comparison of mean thickness of gyri in two groups
by Mehul Sampat 02 Nov '09

02 Nov '09

Hi Folks, If am comparing the mean thickness for certain gyri (pre-central, post-central) in a controls versus patients. I obtain the thickness measurements from lh.aparc.a2009s.stats and rh.aparc.a2009s.stats I was wondering if I need to normalize these thickness measurement with the estimated total intracranial volume (eTIV) ? Or has anyone reported that the these are independent of eTIV ? If so then as I understand I would only need to account for age and gender in any subsequent analysis using GLM. Thanks Mehul

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Making nice images using FreeSurfer
by Estephan Moana 01 Nov '09

01 Nov '09

Hello FreeSurfer experts, I am playing with displaying FEAT output over the 3D pial surface provided by FS. I was wondering if somebody knows how to: 1. See both hemispheres side-by-side at the same time (both pial and inflated, if possible); 2. Make a video of the output 3D brain rotating at a certain axis (x,y or z), and maybe transitioning from pial to inflated surface. This may not really matters for scientific purposes, but it should produce some "wows" during lectures and thesis defense (my goal). AFNI does it, but its rendering option makes the image grainy, resulting in a video with poor resolution. Thank you. Estephan Moana, DDS Graduate Student Oral Biology PhD Program - Neurobiology track School of Dentistry, UNC- Chapel Hill 2140 Old Dental Building, CB# 7455 Chapel Hill, NC 27599 Phone: (919) 966-5680 Fax: (919) 966-5339 moana(a)email.unc.edu

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editing grey matter or white matter
by karlkarl 30 Oct '09

30 Oct '09

Hello, freesurfer experts: I attached one sample picture of the results from autorecon2. In the bottom of right hemisphere, both the red and yellow line shrink, leaving some tissue outside. How should I fix these since it involves both grey matter and white matter editing? thanks Karl _________________________________________________________________ 全新 Windows 7：寻找最适合您的 PC。了解详情。 http://www.microsoft.com/china/windows/buy/

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Re: [Freesurfer] transverse gyrus and intermediate sulcus
by Narly A Golestani 30 Oct '09

30 Oct '09

Hi Chrisophe, Thanks very much for your answer but I'm not sure I understand. I see the below labels in the '?h.aparc.a2005s.annot' label files generated by freesurfer version 4.4 as well as in those generated by freesurfer version 3.0.5: 'S_temporal_transverse' 'G_temp_sup-G_temp_transv_and_interm_S' In the 'default' label file (ie; 'lh.cortex.label' and 'rh.aparc.annot') of the output generated by both of these versions of freesurfer, I see the following labels only: '?h_transversetemporal'. In sum, I'm not sure how the atlases that you've mentioned below relate to the 'default' versus '2005a' versions of the label files, and also how they relate to different version of freesurfer. If the 'atlas2002_simple.gcs' atlas is used to generate the 'default' labels (ie; '?h.cortex.label'), then I'm not sure why I don't see the 'G_temp_sup-G_temp_transv_and_interm_S' amongst the labels generated by freesurfer version 3.0.5. I'm also not clear on how this changed between versions 3.0.5 and 4.4 - I would expect to see different labels between the 2 versions, but I don't. I have another, related question: I would also like to know if there is a way of seeing whether an intermediate sulcus was detected at all or not for a particular brain/hemisphere (eg; there should not be any detected if there is only one transverse temporal gyrus). In other words, I would like to know when freesurfer detected multiple transverse gyri and when it did not. thanks very much in advance, and all the best, Narly. On Thu, 15 Oct 2009, Christophe Destrieux wrote: > Hi Narly > > Hello Christophe, hello all, > > > > I would like to know if the way that the transverse gyrus is labelled in > > freesurfer, and specifically the fact that in the case of multiple > > transverse gyri only the more anterior transverse temporal gyrus (ie; > > Heschl's gyrus) is included, has changed across different releases of > > freesurfer, or if it differs between the different atlases used by > > freesurfer. I ask this because I see a somewhat different pattern of > > results in this part of the brain when comparing output generated by > > freesurfer version 3.0.5 and version 4.4. > > > the changed occured in 2005; but both atalases (atlas2002_simple.gcs and > atlas2005_simple.gcs) were distributed for a while) > > In the 2002 version the parcellation was indeed different : > > * When several transverse temporal gyri were present they were > grouped together in a common label with the sulcus limiting them > (G_temp_sup-G_temp_transv_and_interm_S) > * The sulcus posterior to this label was then labeled > "S_temporal_transverse" > > I hope that it helped > > More generally, I would like to know if there is any version of > > freesurfer, or any atlas, that includes multiple transverse gyri when they > > exist (ie; that does NOT exclude the more posterior one in cases of > > multiple transverse gyri). > > > > > thanks in advance and best wishes, > > Narly. > > > > > >> On Thu, 2009-08-06 at 20:57 +0200, Christophe Destrieux wrote: > >> > >> > >>> Hi Narly > >>> > >>> below are a few explanations on the transverse temporal gyrus in the > >>> a2005 parcellation > >>> > >>> At the superior aspect of the superior temporal gyrus: > >>> > >>> * the transverse temporal *sulcus* limits the planum temporale > >>> (posteriorly) from the transverse temporal gyrus (anteriorly); it > >>> originates at the posterior segment of the lateral sulcus, runs > >>> anterior and lateral and joins the lateral aspect of the temporal > >>> lobe. > >>> > >>> * The transverse temporal gyrus (or Heschl's gyrus) is just anterior > >>> and parallel to the transverse temporal sulcus. Instead of a > >>> single transverse temporal gyrus, several �transverse� temporal > >>> gyri bordered by intermediate sulci may be present. Only the more > >>> anterior transverse temporal gyrus is labeled in Freesurfer, the > >>> posterior ones being included in the planum temporale since they > >>> where shown not to correspond to primary, but to secondary > >>> auditory cortex > >>> > >>> I hope that it helped > >>> > >>> cheers > >>> > >>> -- > >>> Christophe Destrieux > >>> Laboratoire d'Anatomie - Facult� de M�decine - 10 Bd Tonnell� > >>> 37032 Tours - France > >>> tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 > >>> > >>> > >>>> Narly, > >>>> > >>>> I'm forwarding this to Christophe Destrieux, cc'd, who I think can > >>>> answer your question about how that region is labelled. > >>>> > >>>> It is not possible to do translucent viewing in tksurfer. However, it > >>>> is possible in qdec. Just use the load surface and load annotation menu > >>>> options. > >>>> > >>>> Nick > >>>> > >>>> > >>>> On Thu, 2009-08-06 at 16:26 +0100, Narly A Golestani wrote: > >>>> > >>>> > >>>>> Hello, > >>>>> > >>>>> I would like to know more about the automatic labelling of the transverse > >>>>> temporal gyrus is done. I looked at the below article but don't see any > >>>>> details about this structure. > >>>>> > >>>>> https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf > >>>>> > >>>>> I would for example like to know how the boundaries of this structure are > >>>>> defined/determined. > >>>>> > >>>>> Also, when using tksurfer to view labels ('import annotation'), is it > >>>>> possible to make the 3D brain surface (and labels) translucent so that one > >>>>> can more carefully view where this (medial-spanning) gyrus was identified? > >>>>> > >>>>> thanks in advance, > >>>>> Narly. > >>>>> > >>>>> _______________________________________________ > >>>>> Freesurfer mailing list > >>>>> Freesurfer(a)nmr.mgh.harvard.edu > >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>>> > >>>>> > >>>>> > >>>>> > >>>> > >>> > >> > > > > ==================================== > > Narly Golestani > > Institute of Cognitive Neuroscience > > 17 Queen Square > > London WC1N 3AR > > United Kingdom > > Tel: +44 (0)20 7679 7529 > > ==================================== > > > > > > > -- > Christophe Destrieux > Laboratoire d'Anatomie - Facult� de M�decine - 10 Bd Tonnell� > 37032 Tours - France > tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 > > > > ==================================== Narly Golestani Institute of Cognitive Neuroscience 17 Queen Square London WC1N 3AR United Kingdom Tel: +44 (0)20 7679 7529 ====================================

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about the thalamus volume
by zhenxt03 30 Oct '09

30 Oct '09

Hi, I found Left-Thalamus-Proper volume and Right-Thalamus-Proper volume in the aseg.stats file. Do they have some difference between Left-Thalamus-Proper volume and Left thalamus volume? If not, can I use left or right thalamus proper volumes to do some statistics analysis between two groups? Thank you very much! Yours sincerely Xiantong Zhen

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structural morphometric analyses for 50 subjects
by Ritobrato Datta 30 Oct '09

30 Oct '09

Hello All, I have processed about 100 datasets with recon-all (autorecon1, 2and 3) There are 50 subjects, each subject is scanned twice, 19 months apart. So each subject acts as their own control. We only have structural data for these subjects only MPRAGES, one per each scan. No functional data. What kind of structural morphometric analyses can I do using freesurfer ? I mean if I want to see what has changed in each subject between the two sessions ? For each session, we have other data like their blood pressure, gender, age, ambient pressure, ambient temperature etc. For eg, there is a difference in ambient temperature between the first and second scans and I want to see if there is a structural morphometric change in each subject due to this temperature change, can that kind of statistics be done with freesurfer ? How do I remove the effect of other factors to see only the changes due to temperature change ? I have never done this kind of an analyses before, so so maybe freesurfer already has a pipe for this sort of analyses. I dont know. I am looking for any guidance I can get. Please let me know. Thanks a lot, Rito Ritobrato Datta, Ph.D. Post Doctoral Fellow Department of Neurology Center for Functional Neuroimaging University of Pennsylvania School of Medicine 3rd Floor Gates Building 3400 Spruce St. Philadelphia Pa 19104

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Fwd: FreeSurfer Error: bits = 0 not supported.
by Jordi Delgado 30 Oct '09

30 Oct '09

---------- Forwarded message ---------- From: Jordi Delgado <jordidem(a)pic.es> Date: 2009/10/30 Subject: FreeSurfer Error: bits = 0 not supported. To: freesurfer(a)nmr.mgh.harvard.edu Hello*, * My name is Jordi Delgado, I work with FreeSurfer on a cluster of machines. Yesterday I sent some subjects to process and for three of them I recived in the Output Log from PBS the following message: * Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.1 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.1 INFO: SUBJECTS_DIR is /nfs/arpon/PROJCT/FXTAS/proc/FREESURFER/OutPBS Actual FREESURFER_HOME /nfs/arpon/SOFTWR/freesurfer Linux td172.pic.es 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:12:52 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux /nfs/arpon/PROJCT/FXTAS/proc/FREESURFER/OutPBS/PCC_030 mri_convert /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030/PCC_030_0001 /nfs/arpon/PROJCT/FXTAS/proc/FREESURFER/OutPBS/PCC_030/mri/orig/001.mgz mri_convert /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030/PCC_030_0001 /nfs/arpon/PROJCT/FXTAS/proc/FREESURFER/OutPBS/PCC_030/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030/PCC_030_0001... Starting DICOMRead2() dcmfile = /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030/PCC_030_0001 dcmdir = /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030 WARNING: tag ImageNumber not found WARNING: tag image orientation not found Ref Series No = 301 ERROR: bits = 0 not supported. Send email to freesurfer(a)nmr.mgh.harvard.edu Linux 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:12:52 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Oct 29 18:26:01 CET 2009* After revising the freesurfer implementation and verify that other subjects have been processed correctly I noted that three subjects start their slices numeration with 0001 up to 0172 and the rest started (the correctly finished subjects) by 0002 up to 0171. So I searched this error in the freeSurfer wiki and google and I didn't found anything. What is happening? Is an image problem? Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edificio D E-08193 Bellaterra, Barcelona Tel: +34 93 581 33 22 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edificio D E-08193 Bellaterra, Barcelona Tel: +34 93 581 33 22 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html

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