[Freesurfer] Please forward to your list: Now seeking applications for 2 research positions at Douglas Brain Imaging Center - McGill, Montreal, Qc
Please see message below regarding 2 research positions available at the Douglas Brain Imaging Center: _ Research positions available at the Douglas Brain Imaging Centre Douglas Brain Imaging Centre, Douglas Mental Health University Institute McGill University, 6785 LaSalle Blvd., Montreal, Quebec, H4H 1R3, Canada http://www.douglas.qc.ca/page/bic The Douglas Brain Imaging Centre, Douglas Mental Health University Institute, Montreal, Canada, was established in 2011 and houses a Siemens 3T Magnetom Trio MRI Scanner for human research, and a Bruker 7T Biospec 70/30 USR MRI Scanner for small animal research, and labs specialized in optogenetics, electroencephalography (EEG) and transcranial magnetic stimulation (TMS). The Douglas BIC is a vibrant research centre composed of 9 research labs which host 40+ student and post-doctoral researchers. The Centre is also composed of core non-academic staff who ensure quality imaging and data management services to researchers and students. The BIC's focus is on clinical and pre-clinical neuroscience research in the area of mental health and is actively involved in 23 academic and industry sponsored research projects. The Douglas BIC is now expanding its functional MRI research expertise. The Centre is seeking to fill two positions in the next year: 1) a full-time Research Assistant position for applying current fMRI analysis tools to human imaging data, and 2) a full-time Post-doctoral Research Fellow focused on developing novel small animal (mouse and rat) fMRI analysis tools. Below is a list of the specific requirements for these two positions. Full-time Research Assistant Start date: April 1, 2015 The Douglas BIC is seeking a full-time research assistant specialized in MRI image analysis who will work with the Centre's Director, in collaboration with other Principal Investigators, in conducting fMRI resting state connectivity analysis, and univariate and/or multivariate task-based fMRI analysis on human fMRI data using existing software packages. The candidate will also be responsible for providing training support to the Centre's students on conducting fMRI analyses. All applicants must be eligible to work in Canada. In addition, the successful candidate must have: * A M.Sc., or a B.Sc. with excellent research experience, in the area of either: psychology, neuroscience, biology, engineering or computer science * Experience in FMRI image processing and analysis using one or more of the following software packages: SPM, FSL, BrainVoyager, MRIcro, AFNI * Experience working on Linux operating systems * Experience in using Matlab * Experience with SPSS and MS Office Suite * Research interest in neuroscience and mental health * Good written and oral communication skills in English * Ability to work well in a team Preferred Qualifications: * Experience in programming using Matlab, Python, C/C++, R. * Ability to work independently and problem solve The salary will commiserate with experience. Post-doctoral Research Fellow Start date: October 1, 2015. The Douglas BIC is seeking a Post-doctoral Researcher with a strong background in neuroscience and computer programming who is interested in developing analysis tools for small animal fMRI. The successful candidate must have: * Ph.D. in Neuroscience /Computer Science/Systems Engineering, or related field * Experience in fMRI methods development * Excellent programming skills in one or more of the following: Matlab, Python, C/C++, R. * Excellent writing and communication skills * A record of scientific publication consistent with his/her stage of career development * Project leadership skills Preferred Qualifications: * Experience or interest in pre-clinical neuroscience research in the field of mental health * Ability to work in a team Interested applicants are invited to please send electronically a: i) Cover Letter, ii) Curriculum Vitae, and iii) arrange to have 3 reference letters sent to: Tayna Bardati (tayna.bard...@douglas.mcgill.camailto:tayna.bard...@douglas.mcgill.ca), Administrative Assistant to the Director (Dr. M. N. Rajah) - Douglas CIC, Douglas Mental Health University Institute, 6875 LaSalle Blvd, Montreal, QC, H4H 1R3, Canada All outstanding applicants are encouraged to apply; however, in accordance with Canadian immigration requirements, priority will be given to Canadian citizens and permanent residents of Canada. The Douglas Institute is committed to equity in employment and diversity. It welcomes applications from indigenous peoples, visible minorities, ethnic minorities, persons with disabilities, women, persons of minority sexual orientations and gender identities and others who may contribute to further
Re: [Freesurfer] Map volume label to surface label
The registration file maps between the FS anatomical in conformed space and the label volume. If they are the same voxel-for-voxel space, then use --regheader, otherwise use bbregister to get the registration file and pass that to vol2surf On 2/16/15 11:18 AM, Muhammad Razib wrote: Hi Bruce, Thanks for the reply. I am not sure if I am fundamentally wrong at some places. I am new to freesurfer, previously I processed some .nii files with recon-all command which created surfaces like lh.pial/rh.pial etc. After that I did cortical percellation. But the data that I am using now are IBSR (http://www.nitrc.org/projects/ibsr) manually labeled volume data (contains img/hdr/mat file). But I want to get labeled surface like lh.pial/rh.pial from this labeled volume data. I was looking into mri_vol2surf command, but it needs a parameter --srcreg which I am not sure about. How can I get this registration file? Do I need to create this using freesurfer? I highly appreciate your time and suggestion. Thanks On Tue, Feb 10, 2015 at 9:54 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: If the labels are a segmentation volume, then you'll need to run mri_vol2surf with --interp nearest. doug On 2/10/15 6:39 PM, Bruce Fischl wrote: Hi Razib yes, I think mri_label2label will do this if you have reconstructed the surfaces. cheers Bruce On Tue, 10 Feb 2015, Muhammad Razib wrote: Hi, I am wondering is there a way in freesurfer to map manually labeled IBSR MRI .img/.hdr volume files to freesurfer surface file (e.g. lh.pial/rh.pial etc.) keeping the original labels? Thanks, Razib ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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. -- Muhammad Razib PhD Student in Computer Science Florida International University Miami, FL, USA ___ 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] Map volume label to surface label
Hi Bruce, Thanks for the reply. I am not sure if I am fundamentally wrong at some places. I am new to freesurfer, previously I processed some .nii files with recon-all command which created surfaces like lh.pial/rh.pial etc. After that I did cortical percellation. But the data that I am using now are IBSR (http://www.nitrc.org/projects/ibsr) manually labeled volume data (contains img/hdr/mat file). But I want to get labeled surface like lh.pial/rh.pial from this labeled volume data. I was looking into mri_vol2surf command, but it needs a parameter --srcreg which I am not sure about. How can I get this registration file? Do I need to create this using freesurfer? I highly appreciate your time and suggestion. Thanks On Tue, Feb 10, 2015 at 9:54 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: If the labels are a segmentation volume, then you'll need to run mri_vol2surf with --interp nearest. doug On 2/10/15 6:39 PM, Bruce Fischl wrote: Hi Razib yes, I think mri_label2label will do this if you have reconstructed the surfaces. cheers Bruce On Tue, 10 Feb 2015, Muhammad Razib wrote: Hi, I am wondering is there a way in freesurfer to map manually labeled IBSR MRI .img/.hdr volume files to freesurfer surface file (e.g. lh.pial/rh.pial etc.) keeping the original labels? Thanks, Razib ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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. -- Muhammad Razib PhD Student in Computer Science Florida International University Miami, FL, USA ___ 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] Entorhinal Cortex segmentation and volume
Yes, that is normal On 2/16/15 11:42 AM, Melina Lehnerer wrote: Thank you both for your respond. 1. I have attached you some pictures. Like douglas wrote it corresponds to white matter in aseg, but is more often labelled as none than cortex unknown. So is this normal and can I trust those borders? Or would you rather advise to control aseg and aparc segmentation to estimate the entorhinal cortex segmentation? 2. You're right, Bruce, in freeview the exvivo label it just follows the surface. So I'll try mri_label2vol. Cheers Melina Am 16.02.2015 um 16:33 schrieb Douglas Greve: On 2/16/15 9:31 AM, Bruce Fischl wrote: Hi Melina 1. Can you send us a picture? I'm not sure given your description, although the surfaces can be arbitrary in the hippocampus/amygdala and should be ignored there. This corresponds to the cortex unknown label in aparc (and is probably labeled WM in the aseg). This is normal. 2. You should be able to use mri_label2vol for this. Note that you can load the label itself directly into freeview if you want without needing to run label2vol (but it will follow the white surface I believe and not fill the ribbon) cheers Bruce On Mon, 16 Feb 2015, Melina Lehnerer wrote: Hi experts, I'm rather unexperienced with freesurfer so please excuse my basic requests. 1. I controlled the segmentation of the entorhinal cortex (EC) in over 50 subjects following the borders described in Fischl 2009 (Predicting the location of EC from MRI) with tkmedit [mri name] brainmask.mgz -seg aparc-aseg.mgz. I noticed (esp. in the coronar slices and in approximately every mri) brain tissue between amygdala/ hippocampus/ temporalpole and the EC labelled as none or ctx-?h-unknown. Has anything gone wrong with the segmentation? Or is a label (e.g. perirhinal cortex) not loaded? 2. Is there a possibility to visualize the EC volume in freeview or tkmedit from the exvivo.stats or exvivo.label file? I would like to compare it to the other EC volume because they have very different volumes. In the mail archive were similar questions about that but you haven't answered them yet. Many thanks in advance, Melina ___ 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 ___ 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 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.
[Freesurfer] use of RFT script for cluster correction of results from lme analysis
Hi Don, Jorge, and list, I would like to do cluster-size based family-wise error correction on the results of a longitudinal analysis done with the lme toolbox. As Jorge told me that if I don't use spatiotemporal models, the use of RFT should be valid, I want to use the script posted on the list by Don (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg05717.html) and have some questions about the parameters to use: - when I want to correct for all vertices in the ?h.cortex.label, is it correct to take 'nvert' and 'surface area' as output by the command ```mris_info fsaverage/surf/?h.white``` - what command would I use to get these parameters for a smaller label (that merges only parcellations important for the subject of my study)? - for 'fwhm', do I just take the smoothing kernel width I used when preparing the data for group analysis? - how do I determine 'df' as they vary over the different vertices?. Would I just take the average or is there a smarter way? BTW, from experimenting with wildly different dfs (e.g., 10 vs 1000) dfs it seems that they result only in very litte differences in the FWE corrected cluster size output by the script. Is that correct? Thank you very much for your help! Janosch ___ 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] Talarach to MNI coordinates program?
Dear Freesurfers, Was wondering if anyone had any simple programs to convert the freesurfer Talaraich co-ordinates to MNI? Best wishes, Alex === Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News World Report (2014). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ 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] Changing wstresh and removing wsg-atlas - consequences?
Hi Silas you should certainly try to avoid a group-by-processing parameters bias. Is there a reason that one group would require different parameters than another? cheers Bruce On Mon, 16 Feb 2015, Silas wrote: Hi Freesurfer team, I'm currently making an structural analysis using freesurfer. In the analysis i'm comparing 3 groups; 2 patient groups with different reactions to a certain type of medication and a healthy control group. In the freesurfer pipeline i'm changing the parameters wsthresh and wsgatlas in order to obtain a better fitted pial surface and white matter surface - and i was wondering if changing these parameters affect the comparability of the 3 groups (if e.g. i would like to investigate the inferior frontal gyrus)? Best, Silas ___ 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] Changing wstresh and removing wsg-atlas - consequences?
Hi Silas, Changing the wsthresh and wsgatlas parameters only affect the brainmask (which is, among other things, used to limit how far the pial surface is allowed to grow). This shouldn't affect the white matter. if your data contrast is good, you generally wont see much affect from adjusting these parameters. However, if the contrast is bad you need to inspect your brainmasks carefully, to make sure they improved (without removing actual brain from the image). Furthermore, in this case it is likely you'll also need to edit the brainmasks manually. To answer your question: Whenever you modify the parameters, and in particular if you need to edit brainmasks, you introduce a bias in your study (your qualitative evaluation of how good the brainmasks / pial surfaces are). You need to consider if adjusting brainmasks is better than letting the pipeline do its job - which boils down to the number of subjects you have. The more you have, the more robust your statistics will be, and the more likely it is that you can leave everything as it is. However, If you have few subjects, bad data quality (and in turn, brainmask quality) can really impact your pial surface, and then it may be best to adjust the masks. We can talk more at the hospital if you need further discussion, and also look at your data ;-) Best, Christian On 02/16/2015 01:54 PM, Silas wrote: Hi Freesurfer team, I'm currently making an structural analysis using freesurfer. In the analysis i'm comparing 3 groups; 2 patient groups with different reactions to a certain type of medication and a healthy control group. In the freesurfer pipeline i'm changing the parameters wsthresh and wsgatlas in order to obtain a better fitted pial surface and white matter surface - and i was wondering if changing these parameters affect the comparability of the 3 groups (if e.g. i would like to investigate the inferior frontal gyrus)? Best, Silas ___ 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 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] Entorhinal Cortex segmentation and volume
Hi Melina 1. Can you send us a picture? I'm not sure given your description, although the surfaces can be arbitrary in the hippocampus/amygdala and should be ignored there. 2. You should be able to use mri_label2vol for this. Note that you can load the label itself directly into freeview if you want without needing to run label2vol (but it will follow the white surface I believe and not fill the ribbon) cheers Bruce On Mon, 16 Feb 2015, Melina Lehnerer wrote: Hi experts, I'm rather unexperienced with freesurfer so please excuse my basic requests. 1. I controlled the segmentation of the entorhinal cortex (EC) in over 50 subjects following the borders described in Fischl 2009 (Predicting the location of EC from MRI) with tkmedit [mri name] brainmask.mgz -seg aparc-aseg.mgz. I noticed (esp. in the coronar slices and in approximately every mri) brain tissue between amygdala/ hippocampus/ temporalpole and the EC labelled as none or ctx-?h-unknown. Has anything gone wrong with the segmentation? Or is a label (e.g. perirhinal cortex) not loaded? 2. Is there a possibility to visualize the EC volume in freeview or tkmedit from the exvivo.stats or exvivo.label file? I would like to compare it to the other EC volume because they have very different volumes. In the mail archive were similar questions about that but you haven't answered them yet. Many thanks in advance, Melina ___ 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.
[Freesurfer] Changing wstresh and removing wsg-atlas - consequences?
Hi Freesurfer team, I'm currently making an structural analysis using freesurfer. In the analysis i'm comparing 3 groups; 2 patient groups with different reactions to a certain type of medication and a healthy control group. In the freesurfer pipeline i'm changing the parameters wsthresh and wsgatlas in order to obtain a better fitted pial surface and white matter surface - and i was wondering if changing these parameters affect the comparability of the 3 groups (if e.g. i would like to investigate the inferior frontal gyrus)? Best, Silas ___ 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] Entorhinal Cortex segmentation and volume
Hi experts, I'm rather unexperienced with freesurfer so please excuse my basic requests. 1. I controlled the segmentation of the entorhinal cortex (EC) in over 50 subjects following the borders described in Fischl 2009 (Predicting the location of EC from MRI) with tkmedit [mri name] brainmask.mgz -seg aparc-aseg.mgz. I noticed (esp. in the coronar slices and in approximately every mri) brain tissue between amygdala/ hippocampus/ temporalpole and the EC labelled as none or ctx-?h-unknown. Has anything gone wrong with the segmentation? Or is a label (e.g. perirhinal cortex) not loaded? 2. Is there a possibility to visualize the EC volume in freeview or tkmedit from the exvivo.stats or exvivo.label file? I would like to compare it to the other EC volume because they have very different volumes. In the mail archive were similar questions about that but you haven't answered them yet. Many thanks in advance, Melina ___ 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] Changing wstresh and removing wsg-atlas - consequences?
Hi Bruce, Thanks for your answer. My data quality isn't always as good as i could have hoped. This unfortunately impairs freesurfers ability to distinguish between grey matter surface, dura and skull. In specific cases I've found it rewarding to change the parameters in order to gain a better fitting of the pial surface to the actual grey matter surface. Afterwards I've made manual editing to obtain the best possible fit. These parameter changes isn't group specific. Would you still avoid changing the parameters? Best, Silas Date: Mon, 16 Feb 2015 09:28:05 -0500 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Changing wstresh and removing wsg-atlas - consequences? Hi Silas you should certainly try to avoid a group-by-processing parameters bias. Is there a reason that one group would require different parameters than another? cheers Bruce On Mon, 16 Feb 2015, Silas wrote: Hi Freesurfer team, I'm currently making an structural analysis using freesurfer. In the analysis i'm comparing 3 groups; 2 patient groups with different reactions to a certain type of medication and a healthy control group. In the freesurfer pipeline i'm changing the parameters wsthresh and wsgatlas in order to obtain a better fitted pial surface and white matter surface - and i was wondering if changing these parameters affect the comparability of the 3 groups (if e.g. i would like to investigate the inferior frontal gyrus)? Best, Silas ___ 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 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] Changing wstresh and removing wsg-atlas - consequences?
Hi Christian, Thanks! My data quality is generally not very good - this i why i'm changing the parameters before starting manual editing (this saves me a lot of work). I just wanted to make sure that it did not affect the atlas more than necessary - making the data incomparable. Lets have a talk at DRCMR - i also have some questions concerning movement artefacts. Best, Silas Date: Mon, 16 Feb 2015 15:28:46 +0100 From: ct...@dtu.dk To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Changing wstresh and removing wsg-atlas - consequences? Hi Silas, Changing the wsthresh and wsgatlas parameters only affect the brainmask (which is, among other things, used to limit how far the pial surface is allowed to grow). This shouldn't affect the white matter. if your data contrast is good, you generally wont see much affect from adjusting these parameters. However, if the contrast is bad you need to inspect your brainmasks carefully, to make sure they improved (without removing actual brain from the image). Furthermore, in this case it is likely you'll also need to edit the brainmasks manually. To answer your question: Whenever you modify the parameters, and in particular if you need to edit brainmasks, you introduce a bias in your study (your qualitative evaluation of how good the brainmasks / pial surfaces are). You need to consider if adjusting brainmasks is better than letting the pipeline do its job - which boils down to the number of subjects you have. The more you have, the more robust your statistics will be, and the more likely it is that you can leave everything as it is. However, If you have few subjects, bad data quality (and in turn, brainmask quality) can really impact your pial surface, and then it may be best to adjust the masks. We can talk more at the hospital if you need further discussion, and also look at your data ;-) Best, Christian On 02/16/2015 01:54 PM, Silas wrote: Hi Freesurfer team, I'm currently making an structural analysis using freesurfer. In the analysis i'm comparing 3 groups; 2 patient groups with different reactions to a certain type of medication and a healthy control group. In the freesurfer pipeline i'm changing the parameters wsthresh and wsgatlas in order to obtain a better fitted pial surface and white matter surface - and i was wondering if changing these parameters affect the comparability of the 3 groups (if e.g. i would like to investigate the inferior frontal gyrus)? Best, Silas ___ 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 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 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] Entorhinal Cortex segmentation and volume
On 2/16/15 9:31 AM, Bruce Fischl wrote: Hi Melina 1. Can you send us a picture? I'm not sure given your description, although the surfaces can be arbitrary in the hippocampus/amygdala and should be ignored there. This corresponds to the cortex unknown label in aparc (and is probably labeled WM in the aseg). This is normal. 2. You should be able to use mri_label2vol for this. Note that you can load the label itself directly into freeview if you want without needing to run label2vol (but it will follow the white surface I believe and not fill the ribbon) cheers Bruce On Mon, 16 Feb 2015, Melina Lehnerer wrote: Hi experts, I'm rather unexperienced with freesurfer so please excuse my basic requests. 1. I controlled the segmentation of the entorhinal cortex (EC) in over 50 subjects following the borders described in Fischl 2009 (Predicting the location of EC from MRI) with tkmedit [mri name] brainmask.mgz -seg aparc-aseg.mgz. I noticed (esp. in the coronar slices and in approximately every mri) brain tissue between amygdala/ hippocampus/ temporalpole and the EC labelled as none or ctx-?h-unknown. Has anything gone wrong with the segmentation? Or is a label (e.g. perirhinal cortex) not loaded? 2. Is there a possibility to visualize the EC volume in freeview or tkmedit from the exvivo.stats or exvivo.label file? I would like to compare it to the other EC volume because they have very different volumes. In the mail archive were similar questions about that but you haven't answered them yet. Many thanks in advance, Melina ___ 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 ___ 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] Changing wstresh and removing wsg-atlas - consequences?
I think that's ok. In the end you want the best models, you just need to make sure that there is no significant group-by-parameters interaction. Not intervening can also cause a bias. For example if there is atrophy in one group that allows the surfaces to avoid dura but in the other group significant dura is included you will overestimate effect sizes cheers Bruce On Mon, 16 Feb 2015, Silas wrote: Hi Bruce, Thanks for your answer. My data quality isn't always as good as i could have hoped. This unfortunately impairs freesurfers ability to distinguish between grey matter surface, dura and skull. In specific cases I've found it rewarding to change the parameters in order to gain a better fitting of the pial surface to the actual grey matter surface. Afterwards I've made manual editing to obtain the best possible fit. These parameter changes isn't group specific. Would you still avoid changing the parameters? Best, Silas Date: Mon, 16 Feb 2015 09:28:05 -0500 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Changing wstresh and removing wsg-atlas - consequences? Hi Silas you should certainly try to avoid a group-by-processing parameters bias. Is there a reason that one group would require different parameters than another? cheers Bruce On Mon, 16 Feb 2015, Silas wrote: Hi Freesurfer team, I'm currently making an structural analysis using freesurfer. In the analysis i'm comparing 3 groups; 2 patient groups with different reactions to a certain type of medication and a healthy control group. In the freesurfer pipeline i'm changing the parameters wsthresh and wsgatlas in order to obtain a better fitted pial surface and white matter surface - and i was wondering if changing these parameters affect the comparability of the 3 groups (if e.g. i would like to investigate the inferior frontal gyrus)? Best, Silas ___ 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 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] Using TRACULA ROI for image in diffusionspace
Dear TRACULA experts, I wonder if you could please assist me in extracting tract values from an image I transferred to diffusion space. I ran TRACULA on my DTI dataset, however from other structural images I aim to extract values for tracts as well. I also extracted DTI derived measures from these tracts of my DTI data (FA,MD,RD,AD), using this command: trac-all -stat -c dmrirc And now I wonder whether I could add another line to the source code of the stats command so that it would output values from that other image I have in diffusion space. Best wishes and thank you, Barbara Anne ___ 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.
