Re: [Freesurfer] fsaverage
hi, that line from the wiki appears to be in tcsh syntax, you are using bash, which is the default shell of most operating systems. you can try either in bash, like this: if [ ! -e fsaverage ]; then ln -s $FREESURFER_HOME/subjects/fsaverage; fi ...or in tcsh, which you might need to install first, then invoke it, like: tcsh if (! -e fsaverage) ln -s $FREESURFER_HOME/subjects/fsaverage regards, andreas On Wednesday, March 28, 2012 12:40:38 Ahmed, F, Me fah...@sun.ac.za wrote: Hello, I'm trying to run qdec on my own data and I'm trying to create fsaverage. Following the wiki tutorial, I copied the command: if (! -e fsaverage) ln -s $FREESURFER_HOME/subjects/fsaverage but I got the following error: bash: syntax error near unexpected token `ln' Can anyone help me in understanding why this happened? Thanks very much, Fatima E-pos vrywaringsklousule Hierdie e-pos mag vertroulike inligting bevat en mag regtens geprivilegeerd wees en is slegs bedoel vir die persoon aan wie dit geadresseer is. Indien u nie die bedoelde ontvanger is nie, word u hiermee in kennis gestel dat u hierdie dokument geensins mag gebruik, versprei of kopieer nie. Stel ook asseblief die sender onmiddellik per telefoon in kennis en vee die e-pos uit. Die Universiteit aanvaar nie aanspreeklikheid vir enige skade, verlies of uitgawe wat voortspruit uit hierdie e-pos en/of die oopmaak van enige l?ers aangeheg by hierdie e-pos nie. E-mail disclaimer This e-mail may contain confidential information and may be legally privileged and is intended only for the person to whom it is addressed. If you are not the intended recipient, you are notified that you may not use, distribute or copy this document in any manner whatsoever. Kindly also notify the sender immediately by telephone, and delete the e-mail. The University does not accept liability for any damage, loss or expense arising from this e-mail and/or accessing any files attached to this e-mail. ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] TRACULA and CVS space
Hi, I would like to know if for a probabilistic tractrography using TRACULA I can use the CVS space as a common template to register the diffusion data instead of MNI template. How I should change for the CVS space the following: set doregmni = 1 which is the default for the MNI space. If I want to use both MNI template and CVS template for comparison purposeshow this can be done? THANKS. Antonella___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] TRACULA and CVS space
Hi Antonella, We've not released CVS template /Priors for tracula yet. You can only use MNI template for tracula now. We're still testing CVS. Thanks, Priti Hi, I would like to know if for a probabilistic tractrography using TRACULA I can use the CVS space as a common template to register the diffusion data instead of MNI template. How I should change for the CVS space the following: set doregmni = 1 which is the default for the MNI space. If I want to use both MNI template and CVS template for comparison purposeshow this can be done? THANKS. Antonella___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] TRACULA and CVS space
Note that tracula doesn't extract from the atlas the exact spatial location of the tracts. It only extracts which anatomical labels are the neighbors of the tract at each point along its trajectory. So it's not as sensitive to misregistration as a voxel-based analysis would be. Our paper discusses all this: http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2011.00023/abstract On Thu, 29 Mar 2012, Antonella Kis wrote: Hi, I would like to know if for a probabilistic tractrography using TRACULA I can use the CVS space as a common template to register the diffusion data instead of MNI template. How I should change for the CVS space the following: set doregmni = 1 which is the default for the MNI space. If I want to use bo th MNI template and CVS template for comparison purposes how this can be don e? THANKS. Antonella ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] [FREESURFER] atlas applicability. (fwd)
Hi Cheol, I am using freesurfer for patients with various neural disease. I wonder the the freesurfer atlas is applicable to them: dementia (with Lewy bodies, DLB), epilepsy, schizophrenia, ADHD, Alzheimer, stroke. (I know some studies already used freesurfer for some of the diseases in the list,) I believe epilepsy patients with lobectomy cannot be applicable. If the malformation or the difference between normal control acquisitions and your scans is significant the FS pipeline, using the FS atlas is not going to be successful. Withuot seeing your data I cannot tell which population from the above is going to be affected, but if in doubt just try processing one or two representative samples from the different populations and assess how successful the processing is. Also is there age limit for the freesurfer atlas? How young can the atlas work for? 4 year-old? 6 year-old? or more than 10 year-old? How about the upper bound? 80 year-old? The lower bound, in our experience, is about 4-5 yrs. Of course, it depends on your data quality but we had success all the way down to that age. I am not aware of any upper limits. Again, if you are processing these kind of extreme populations, make sure that you inspect the outcome of the FS recon pipeline carefully before proceeding with any type of analysis. Lilla___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] sulci problem
hi all i use mri_anot2label to extract sulci, is there a tool allowing to keep just the deepest line of the sulcus and if possible get the list of talairach coordinates of that line's points. thanks a lot for your help ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] sulci problem
not trivially, sorry. You could run nonmaximum suppression on the ?H.sulc files I guess On Thu, 29 Mar 2012, LAOUCHEDI MAKHLOUF wrote: hi all i use mri_anot2label to extract sulci, is there a tool allowing to keep just the deepest line of the sulcus and if possible get the list of talairach coordinates of that line's points. thanks a lot for your help ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] roi-to-roi functional connectivity analysis
Hi Surfers, Has anyone done ROI-to-ROI functional connectivity analysis using Freesurfer? Current FC pipeline computes the seed-to-voxel correlation for each voxel and thus generates a whole brain correlation map. Is there an easy way to compute the 0-lag correlation between the average time course of two ROIs? One way I presume can work is to take the average time courses generated from the fcseed-sess and do it by hand. For example, just compute the correlation coefficient between lh.hippo.dat and rh.hippo.dat. But does that regress out the white matter and ventricles? Is there a way to do this properly? What should go to the mkanalysis-sess in this case? Thank you for your help. Lingqiang -- Lingqiang Kong Ph.D candidate Auditory Neuroscience Laboratory Perceptual Neuroimaging Laboratory Boston University 677 Beacon St. Boston, MA 02215 http://www.cns.bu.edu/~shinn/ANL/index.html http://people.bu.edu/fmri/ ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] method for detecting neighboring labels?
Is there a way to output a list of all the labels within a given annotation file which share a border with another specified label? Thank you very much, David ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] method for detecting neighboring labels?
not that I know of, sorry On Thu, 29 Mar 2012, David Grayson wrote: Is there a way to output a list of all the labels within a given annotation file which share a border with another specified label? Thank you very much, David ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] [FREESURFER] atlas applicability. (fwd)
Dear Lilla I appreciate your answers. It was very helpful. Just another follow-up question. I think freesurfer itself ended without errors and the skull-stripped and surfaces look okay. I think in the recommended reconstruction Pipeline, check segmentation is related to checking atlas worked. Still, I wonder there is a gold standard to check the atlas (Deksian atlas) works okay. . Thanks again! Best Cheol Cheol Han, Ph.D Computational Neuroscience and Neuroinformatics Department of Brain and Cognitive Sciences Seoul National University Korea On Fri, Mar 30, 2012 at 2:46 AM, Lilla Zollei lzol...@nmr.mgh.harvard.eduwrote: Hi Cheol, I am using freesurfer for patients with various neural disease. I wonder the the freesurfer atlas is applicable to them: dementia (with Lewy bodies, DLB), epilepsy, schizophrenia, ADHD, Alzheimer, stroke. (I know some studies already used freesurfer for some of the diseases in the list,) I believe epilepsy patients with lobectomy cannot be applicable. If the malformation or the difference between normal control acquisitions and your scans is significant the FS pipeline, using the FS atlas is not going to be successful. Withuot seeing your data I cannot tell which population from the above is going to be affected, but if in doubt just try processing one or two representative samples from the different populations and assess how successful the processing is. Also is there age limit for the freesurfer atlas? How young can the atlas work for? 4 year-old? 6 year-old? or more than 10 year-old? How about the upper bound? 80 year-old? The lower bound, in our experience, is about 4-5 yrs. Of course, it depends on your data quality but we had success all the way down to that age. I am not aware of any upper limits. Again, if you are processing these kind of extreme populations, make sure that you inspect the outcome of the FS recon pipeline carefully before proceeding with any type of analysis. Lilla 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/**compliancelinehttp://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. ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] [FREESURFER] atlas applicability. (fwd)
Hi Cheol, I am a bit confused by your question. The atlases that we use help with the segmentation on the surface reconstruction steps when we process a new volume. If the outcomes look resonable to you, then all is good. Did I answer your question? Lilla On Fri, 30 Mar 2012, Cheol Han wrote: Dear Lilla I appreciate your answers. It was very helpful. Just another follow-up question. I think freesurfer itself ended without errors and the skull-stripped and surfaces look okay. I think in the recommended reconstruction Pipeline, check segmentation is related to checking atlas worked. Still, I wonder there is a gold standard to check the atlas (Deksian atlas) works okay. . Thanks again! Best Cheol Cheol Han, Ph.D Computational Neuroscience and Neuroinformatics Department of Brain and Cognitive Sciences Seoul National University Korea On Fri, Mar 30, 2012 at 2:46 AM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi Cheol, I am using freesurfer for patients with various neural disease. I wonder the the freesurfer atlas is applicable to them: dementia (with Lewy bodies, DLB), epilepsy, schizophrenia, ADHD, Alzheimer, stroke. (I know some studies already used freesurfer for some of the diseases in the list,) I believe epilepsy patients with lobectomy cannot be applicable. If the malformation or the difference between normal control acquisitions and your scans is significant the FS pipeline, using the FS atlas is not going to be successful. Withuot seeing your data I cannot tell which population from the above is going to be affected, but if in doubt just try processing one or two representative samples from the different populations and assess how successful the processing is. Also is there age limit for the freesurfer atlas? How young can the atlas work for? 4 year-old? 6 year-old? or more than 10 year-old? How about the upper bound? 80 year-old? The lower bound, in our experience, is about 4-5 yrs. Of course, it depends on your data quality but we had success all the way down to that age. I am not aware of any upper limits. Again, if you are processing these kind of extreme populations, make sure that you inspect the outcome of the FS recon pipeline carefully before proceeding with any type of analysis. Lilla 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. ___ Freesurfer mailing list Freesurfer@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.
[Freesurfer] About the sample data
Dear All, I can't uncompress the data long-tutorial.tar.gz with command tar xzvf /mnt/workplace/long-tutorial.tar.gz /mnt/workplace. How can I uncompress the data? ___ Freesurfer mailing list Freesurfer@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.
Re: [Freesurfer] [FREESURFER] atlas applicability. (fwd)
Dear Lilla Yes, It is clear now! Best Cheol Cheol Han, Ph.D Computational Neuroscience and Neuroinformatics Department of Brain and Cognitive Sciences Seoul National University Korea On Fri, Mar 30, 2012 at 8:40 AM, Lilla Zollei lzol...@nmr.mgh.harvard.eduwrote: Hi Cheol, I am a bit confused by your question. The atlases that we use help with the segmentation on the surface rec onstruction steps when we process a new volume. If the outcomes look resonable to you, then all is good. Did I answer your question? Lilla On Fri, 30 Mar 2012, Cheol Han wrote: Dear Lilla I appreciate your answers. It was very helpful. Just another follow-up question. I think freesurfer itself ended without errors and the skull-stripped and surfaces look okay. I think in the recommended reconstruction Pipeline, check segmentation is related to checking atlas worked. Still, I wonder there is a gold standard to check the atlas (Deksian atlas) works okay. . Thanks again! Best Cheol Cheol Han, Ph.D Computational Neuroscience and Neuroinformatics Department of Brain and Cognitive Sciences Seoul National University Korea On Fri, Mar 30, 2012 at 2:46 AM, Lilla Zollei lzol...@nmr.mgh.harvard.edu wrote: Hi Cheol, I am using freesurfer for patients with various neural disease. I wonder the the freesurfer atlas is applicable to them: dementia (with Lewy bodies, DLB), epilepsy, schizophrenia, ADHD, Alzheimer, stroke. (I know some studies already used freesurfer for some of the diseases in the list,) I believe epilepsy patients with lobectomy cannot be applicable. If the malformation or the difference between normal control acquisitions and your scans is significant the FS pipeline, using the FS atlas is not going to be successful. Withuot seeing your data I cannot tell which population from the above is going to be affected, but if in doubt just try processing one or two representative samples from the different populations and assess how successful the processing is. Also is there age limit for the freesurfer atlas? How young can the atlas work for? 4 year-old? 6 year-old? or more than 10 year-old? How about the upper bound? 80 year-old? The lower bound, in our experience, is about 4-5 yrs. Of course, it depends on your data quality but we had success all the way down to that age. I am not aware of any upper limits. Again, if you are processing these kind of extreme populations, make sure that you inspect the outcome of the FS recon pipeline carefully before proceeding with any type of analysis. Lilla 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/**compliancelinehttp://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. ___ Freesurfer mailing list Freesurfer@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.
