[Freesurfer] FreeSurfer Course to be held in Sao Paulo, Brazil
Hi everyone, There will be a FreeSurfer course held in Sao Paulo, Brazil on March 9th. It will be taught by 4 of our FreeSurfer team members. Please see the Sao Paulo section of our website for links to more information, who to contact with questions, and how to register: https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription Allison ___ 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] FreeSurfer Course Registration now open!
The Freesurfer group is offering a four-day Freesurfer Tutorial and Workshop September 26th to 29th, 2016 at the Martinos Center in Charlestown, MA. You can register for the course on our course website: https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription Details about the content of the course, the location, registration fees, accepted payment types, and nearby hotels is currently on the website above. Please read the above page in its entirety before registering and before sending questions. If you are not one of the first 50 to register, you will be put on a waiting list and will be notified if a spot becomes available. *Do not submit a payment or make travel arrangements until you have received an email confirmation that you successfully secured a seat in the course. Allison Stevens > Lab Manager > FreeSurfer Development Team > Laboratory for Computational Neuroimaging > Massachusetts General Hospital > Athinoula A. Martinos Center for Biomedical Imaging > Bldg. 149, 13th Street, CNY 2301 > Charlestown, MA 02129 ___ 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] hippocampus region in an atlas?
The entire hippocampus is currently labeled by default in the recon-all stream. You can see it in the aseg.mgz (in the mri directory) and find volume information in stats/aseg.stats. To get the hippocampal subfields you have to run recon-all with an additional flag. This is documented here: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation Allison On Tue, 19 Nov 2013, Gregg, Brian E. wrote: Hello, I didn’t see hippocampus listed in the Desikan-Killiany, Destrieux, or DKTatlas40 atlases. Is there an existing atlas that contains the hippocampal subfields? If not, what options exist for getting the hippocampus into an atlas? Thank you, Brian ___ 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] how to obtain subjects cortical thickness and then analyze unpair t-test
Hi Rujing, If you are looking for the cortical thickness measures of a subject, you can find it in that subject's freesurfer directory in the 'stats' folder. In there, you will find a file called ?h.aparc.stats - one for each hemisphere. Within the stats file, you'll see the Average thickness for various cortical regions as well as Mean Thickness of the entire cortex towards the top. The stats for the cortical regions determined by the Destrieux atlas are in the same directory. I suggest looking at the ROI Analysis slides on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial And the tutorial about how to get the stats into a spreadsheet for analysis here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI Please be sure to check over your data before analysis to make sure there are no errors that will affect your study. Allison On Tue, 19 Nov 2013, Rujing Zha wrote: Dear all, Ater recon-all,which image can I select to group t-test? And do they need process in advance? Thanks very much. All the best. 2013-11-19 __ Rujing Zha ___ 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] Volumetric data for GM,WM,CSF.
Hi Saurabh, That information is automatically calculated for you by FreeSurfer. You can find more information about it here: https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats Allison On Wed, 26 Feb 2014, Saurabh Thakur wrote: Hi Freesurfer expert, I am looking for just volumetric quantity of GM,WM,CSF. Can u suggest some commands tat i used or explore so that i get volumetric data. Presently value for subject Bert i m getting: Right now i m working on mri_segstats >giving me vol of white matter by using wmparc.stats Total cortical white matter volume, 484479.305031, mm^3 mri_segstats-> giving me vol of grey matter by using aseg.stats Total gray matter volume, 655593.521190, mm^3 If i wanted to have all the value in one single window/file. cheers Saurabh Thakur ___ 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] The FreeSurfer lab is seeking Research Technicians
Please see the job descriptions at the following links: https://surfer.nmr.mgh.harvard.edu/fswiki/ResearchAssistant https://surfer.nmr.mgh.harvard.edu/fswiki/ResearchTechnologist Allison ___ 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] FreeSurfer Course in Copenhagen
FreeSurfer Course Copenhagen 2014 We are pleased to announce a European FreeSurfer Course that will be held from August 11th to 13th 2014 in Copenhagen, Denmark. The course will be organized by the Neurobiology Research Unit, Copenhagen University Hospital and the Department for Computer Science of the University of Copenhagen in cooperation with the Laboratory for Computational Neuroimaging of the Athinoula A. Martinos Center for Biomedical Imaging. The course will be a three-day course for beginners and experienced users of FreeSurfer and the lectures will be held by FreeSurfer developers from the Laboratory for Computational Neuroimaging of the Athinoula A. Martinos Center for Biomedical Imaging. For further information and to register for this course, please visit: https://fscph2014.nru.dk Allison ___ 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] 2 available spots in Boston FreeSurfer course
We have had some last minute drop outs and there are now 2 spots available in the upcoming Boston FreeSurfer course (May 5-7th). If you would like to sign up for these spots, please register here: https://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/register.8263.cgi Note that credit card cannot be used to pay for the course. Also, this course will not have the diffusion analysis component (it will focus on fMRI analysis). Allison ___ 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] 2 available spots in Boston FreeSurfer course
Hi Andrew, Yes you’re down for a spot. Yours wasn’t one of the two :). Allison On Apr 18, 2014, at 3:23 PM, Andrew Gerber wrote: > Dear Allison, > You have me down for a slot, right? I don't want to miss it! :-) > Best, Andrew > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Allison Stevens > Sent: Friday, April 18, 2014 3:16 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] 2 available spots in Boston FreeSurfer course > > We have had some last minute drop outs and there are now 2 spots available in > the upcoming Boston FreeSurfer course (May 5-7th). If you would like to sign > up for these spots, please register here: > https://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/register.8263.cgi > > Note that credit card cannot be used to pay for the course. Also, this course > will not have the diffusion analysis component (it will focus on fMRI > analysis). > Allison > ___ > 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
[Freesurfer] Postdoc position at Martinos Center for Biomedical Imaging
Postdoc position at Martinos Center for Biomedical Imaging - Massachusetts General Hospital / Harvard Medical School The Laboratory for Computational Neuroimaging at the Martinos Center for Biomedical Imaging has a job opening for a post-doctoral fellow to work on modeling cortical layers and boundaries using Magnetic Resonance Imaging (MRI) and Optical Coherence Tomography (OCT). The project will take place at the Martinos Center (http://www.nmr.mgh.harvard.edu/) and will involve developing computational methods with the goal of extracting quantitative information from OCT images and leveraging the information for MRI analysis. Cutting-edge imaging infrastructure for both these modalities is available at the center and will be used for the project. The methods developed will have be to distributed to the research community through widely used Freesurfer software suite. Applicants are expected to have finished their PhD in medical image analysis, computer vision or a related field with a track record of relevant publications. The project requires experience with mathematical modeling and good programming skills in C/C++ and Matlab/Python. Experience with image registration, deformable surfaces/contours, machine vision techniques and neuroimaging are welcome. The postdoctoral fellow will work closely with Bruce Fischl and Ender Konukoglu. Applications must be sent by email to Ender Konukoglu (end...@nmr.mgh.harvard.edu) and contain a CV, list of publications and names of three references. The intended start date for the position is December 2015 however, the exact date is negotiable. ___ 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] August FreeSurfer course in Copenhagen, Denmark
There are still some spots available in the Copenhagen FreeSurfer Course which will be held from August 10th to 12th, 2016. The course will be organized by the Neurobiology Research Unit, Copenhagen University Hospital in cooperation with the Laboratory for Computational Neuroimaging of the Athinoula A. Martinos Center for Biomedical Imaging. The course will be a three-day course for beginners and experienced users of FreeSurfer and the lectures will be held by FreeSurfer developers from the Laboratory for Computational Neuroimaging. For further information and to register for this course, please visit: http://fscph2016.nru.dk/ Please feel free to contact my friends at NRU (cc'd) with any questions. Allison Stevens Lab Manager/Course Organizer Laboratory for Computational Neuroimaging FreeSurfer Development Team ___ 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] Deadline to sign up for Copenhagen Course is near!
Hi everyone, There is just a week and a half left before the deadline to sign up for the FreeSurfer course being held in Copenhagen, Denmark on August 10th through the 12th. The deadline is June 1st. We still have a few places left! You can sign up for one here: https://fscph.nru.dk/registration.html This will be a 3 day course, very similar to the course we hold in Boston twice a year. The course will be taught by Lilla Zollei, Martin Reuter, Emily Lindemer, and myself. If you've had any trouble registering or have any questions, feel free to contact me or Melanie (fs-cph AT nru.dk) Allison ___ 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] recon all question
Hi Rashmi, You can find an explanation of the various measures we offer here: https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats Allison On Fri, 13 Sep 2013, Rashmi Singh wrote: > I am doing volumetric studies where instead of using ICV, I use total brain > volume as a co-variate. This is why I need total brain volume measurements. > Do you suggest that its not a good idea to use mri-binarize of brain.mgz for > calculating it? > Earlier freesurfer experts had suggeted me to use this option. > Rashmi > ___ > > From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] > Sent: Friday, September 13, 2013 9:09 AM > To: Rashmi Singh > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] recon all question > > what do you want to do with the brain volume? Are you really after > ICV/TIV? We use the det. of the jacobian of the tal xform as per Randy > Buckner, and for it we have compared to actual ICV volumes derived from T2 > volumes and manual stripping > > For the FLAIR, we usually get a T2-space based FLAIR that is also 1mm > isotropic. Once you are done with recon-all, you run it again with the > switch -FLAIRpial and it will do a post-hoc surface > deformation to avoid dura. > > cheers > Bruce > > On Fri, 13 Sep 2013, Rashmi Singh wrote: > >> Thank you Bruce ! >> mri_binarize was suggested to me by the freesurfer group, so now I am a > little concerned when you say that this has not been assessed for accuracy. > May you suggest how otherwise do you get the total brain volume ( which you > suggest is more accurate), as this measurement is not present in the > freesurfer output stat files. >> >> May you please elaborate a little more the steps of using T2-FlAIR for > recon all or suggest me where I can find the detail information ( may be on > the website). While scanning we do collect T2-FLAIR that is linked with T1 > for each subject. Is that what you mean by get a T2-FLAIR? Also, what is a > -T2Flair swicht? >> Sorry, with a background of molecular biology and being a novice in image > analysis, it really takes me time and lots of effort to understand imaging > and its analysis. Your guidance is appreciated. >> Thanks, >> >> Rashmi >> >> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] >> Sent: Friday, September 13, 2013 8:46 AM >> To: Rashmi Singh >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: RE: [Freesurfer] recon all question >> >> 1. I don't think I know anyone who has done this, and we haven't assessed >> it for accuracy. >> >> 2. The best thing to do is get a T2-FLAIR and run it with the -T2Flair >> switch after recon-all is done. This does a great job avoiding dura >> >> cheers >> Bruce >> >> >> On Fri, 13 Sep 2013, Rashmi Singh wrote: >> >>> Hey Bruce, >>> I have two more questions. >>> 1) I was suggested to use mri_binarize with brain.mgz to get the total > brain volume. Is there any reference that I can cite regarding use of > mri_binarize to calculate total brain volume. >>> >>> 2)I learnt that using T2 weighted image along with T1 weighted image > from the same scanning session generates a good contrast and gives better > segmentation/parcellation outputs using FreeSurfer. >>> May the FreeSurfer experts guide me through this. >>> >>> Thanks, >>> Rashmi >>> >>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] >>> Sent: Thursday, September 12, 2013 5:27 PM >>> To: Rashmi Singh >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] recon all question >>> >>> Hi Rashmi >>> >>> putting them in the orig folder with those numbers will get recon-all to >>> do motion correction and averaging. >>> >>> cheers >>> Bruce >>> On Thu, 12 Sep 2013, Rashmi Singh wrote: >>> Hello Freesurfer experts, I am doing volumetrics study. During the scan we get 2-3 mprage per scan for a subject. While running the FreeSurfer, if I want to use the three mprages > for that subject as an input file, may I just keep the three mgz files (001.mgz, 002 .mgz and 003.mgz) in the orig folder and run the simple >>> recon all command :=Recon-all -s (subject file name) -all or do I need to > have some additional l flags so that recon all command will use the three > T1 images to get one output file? Thanks, Rashmi >>> >>> >>> 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. >>> >>> >>> >>> >>> >> >> >> > > > > ___ > Freesurfe
[Freesurfer] FreeSurfer Boston Course Registration now open!
The FreeSurfer group is offering a four-day FreeSurfer Tutorial and Workshop, September 25th to September 28th, 2017 at the Martinos Center for Biomedical Imaging in Charlestown, MA. You can find the link to the registration page at the top of our course website: https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription Details about the content of the course, the location, registration fees, accepted payment types, and nearby hotels is currently on the website above. Please read the above page in its entirety before registering and before sending questions. At the course, laptops are provided with FreeSurfer and practice data already installed. Attendees will work in pairs (sharing a laptop). If you are not one of the first 50 to register, you will be put on a waiting list and will be notified if a spot becomes available. We have enrolled people into the course from the waiting list every time we held a course so don't be dismayed if you end up on the waiting list. Allison Stevens Lab Manager/Course Organizer FreeSurfer Development Team Laboratory for Computational Neuroimaging Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging ___ 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] Is it poosible to redistribute a part of buckner_data for group work?
Dear Kiyotaka, It is okay to distribute the buckner_data we post on our website for tutorial purposes. Allison On Jan 8, 2018, at 6:35 AM, Kiyotaka Nemoto wrote: > Dear FreeSurfer experts, > > We are planning to have a one-day neuroimaging workshop in Japan. One topic > of the workshop is "FreeSurfer troubleshooting", in which we go through the > online tutorial you provide > (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData) in > Japanese language. > > So we would like to use the buckner_data for the workshop. However, the > problem is that some have difficulties downloading the data (It takes more > than 2 days to download...) > > So I'm wondering if we can share the part of buckner_data with attendees for > the workshop in a closed network (via a site with login requirements). I read > through the FreeSurfer license, and README in the buckner_data, but it > doesn't mention about redistributing the data. We would like to respect the > license, so could you let me know if we can redistribute the part of > buckner_data? > > Best regards, > > Kiyotaka > > -- > Kiyotaka Nemoto, M.D., Ph.D. > Associate Professor > Department of Neuropsychiatry > Division of Clinical Medicine, Faculty of Medicine > University of Tsukuba > 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan > E-mail: kiyot...@nemotos.net > ___ > 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] Boston FreeSurfer Course
Hello everyone, The next FreeSurfer Course will be held October 27th-29th at the Martinos Center in Charlestown, Massachusetts. Registration for the course is now open: https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription **Important: If we do not get at least 40 registrants for this course, we will have to cancel it. Details about the content of the course, the location, registration fees, accepted payment types, and nearby hotels is currently on the website above. Please read the above page in its entirety before registering and before sending questions. This course will contain a Diffusion analysis component. fMRI analysis will *not* be taught. Registration is first-come, first-serve. If you are not one of the first 50 to register, you will be put on a waiting list and will be notified if a spot becomes available. *Do not submit a payment or make travel arrangements until you have received an *email confirmation* that you successfully registered for the course. Allison Stevens Lab Manager FreeSurfer Development Team Laboratory for Computational Neuroimaging Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149, 13th Street, CNY 2301 Charlestown, MA 02129 ___ 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] Boston FreeSurfer Course
Hi everyone, We have 31 people signed up for the course so far. A decision about whether this course will be held will be made by Friday. If you were thinking about registering, please do so before then so we know if we've met our minimum requirement of 40 registrants. Thank you, Allison On Mon, 29 Sep 2014, Allison Stevens wrote: > Hello everyone, > The next FreeSurfer Course will be held October 27th-29th at the Martinos > Center in Charlestown, Massachusetts. Registration for the course is now > open: > https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription > > **Important: If we do not get at least 40 registrants for this course, we > will have to cancel it. > > Details about the content of the course, the location, registration fees, > accepted payment types, and nearby hotels is currently on the website > above. Please read the above page in its entirety before registering and > before sending questions. > > This course will contain a Diffusion analysis component. fMRI analysis > will *not* be taught. > > Registration is first-come, first-serve. If you are not one of the first > 50 to register, you will be put on a waiting list and will be notified if > a spot becomes available. *Do not submit a payment or make travel > arrangements until you have received an *email confirmation* that you > successfully registered for the course. > > > > Allison Stevens > Lab Manager > FreeSurfer Development Team > Laboratory for Computational Neuroimaging > Massachusetts General Hospital > Athinoula A. Martinos Center for Biomedical Imaging > Bldg. 149, 13th Street, CNY 2301 > Charlestown, MA 02129 > > ___ > 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] 8 spots remain in the FreeSurfer course
Hello everyone, We have 8 spots remaining in our upcoming FreeSurfer course happening on October 27-29. We will accept late registrations up to the course date; however, since the payment deadline has passed, payment is due immediately upon registration. Details on the course and a link to the registration page can be found here: https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription Note: This course is the only one where we are currently able to accept credit card. This likely won't be an option for future courses. Allison ___ 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] Fwd: Underinclusion of Gray Matter
You could also add a lot more voxels to the wm.mgz (beyond what is wm) and depending on the source of the problem, that could fix it. On Mon, 3 Nov 2014, Bruce Fischl wrote: Hi Christina it's tough to tell from just a single image, but it looks to me like you are missing a bunch of white matter. Can you tell us more about the scan? The typical way you would fix this is by setting some thresholds in mris_make_surfaces using the expert options. Probably max_csf should be lower. If you upload the subject we will take a look cheers Bruce On Mon, 3 Nov 2014, Christina Chen wrote: Hi, Are there any ways to fix underinclusion of gray matter cortical edges when the white matter is fine? Attached is a picture. Thanks, Christina ___ 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] "orig surface" button
Hi Antonella, When you load the files that those buttons are associated with, then they become active. When you loaded the orig surfaces, the orig surface button still was not active? If you choose any button besides the Navigate button, when you left click, that will move the cursor (red crosshair) and then when you click one of the buttons to switch views, the cursor will be located on the same slice as it was in the other view. On Thu, 28 Jul 2011, Antonella Kis wrote: Hi Bruce, Thanks again for your valuable information. I was trying to click on my "orig surface" button in the interface but it is not active. Is there a way that I can enable this option/button? I see more buttons are not active. How I can fix this? Second, using tkmedit, how I can see the same point that I choose in one view for example the coronal view in another view example horizontal view? How I can select this point in one view and make it visible in another view? Thanks, Antonella From: Bruce Fischl To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Wednesday, July 27, 2011 4:35 PM Subject: Re: [Freesurfer] Corrections for the Pial surface Hi Antonella, 1. Can you load the lh.orig or rh.orig surface explicitly and see if it is shown? Is the "orig surface" button clicked in the interface? 2. the hippocampus and amygdala are not neocortical structures and shouldn't be included in the surfaces (in fact, the surfaces in those regions are somewhat arbitrary as they don't have the laminar architecture we are expecting). cheers Bruce On Wed, 27 Jul 2011, Antonella Kis wrote: Hi Bruce, Thank again for your advice. I am not sure about the data collection but I will find out soon. In the mean time I have two more questions: 1). The FS tutorial shows for the surface outlines (by loading the -surfs) three line: the yellow indicating the white surface, the red for the pial and a green line for the orig data. When I plot the surfs I have only the yellow and red line. Can I get the green line somehow? 2). I suppose the two important brain structures, amygdala and hippocampus must be included in the pial surface as a grey matter (I hope I am right) . If they are not enclosed in the pial surface is there a way to resolve this issue? How I should edit the pial surface in this case? How important is to have them enclosed for my cortical thickness studies and for the GLM group analysi? Thank you very much. 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.___ 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] gray matter not incuded in pial surface
There is some white matter there being excluded as well. If you include that, the pial surface will likely grow out and include that gm. On Aug 1, 2011, at 7:37 AM, _andre...@sapo.pt wrote: > Dear FS experts, > > I'm correcting the pial surface when it includes more than it is supposed, > but now I got to a subject where the pial is not incluing what is supposed. > How do I correct this? You can see the problem in the attachd image. > > Thank you! > Andreia > <** brainmask.mgz ** (T1.mgz).png> > ___ > 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] undo pial edits only
Hi Torsten, If you run: recon-all -all -clean-bm -s subjid This should trask all the edits you made to the brainmask volume and make a new one to replace that. It will keep all your other edits. Allison On Tue, 4 Oct 2011, Torsten Ruest wrote: > to correct the pial surface for incorrect assignment of head tissue, I > edit the brainmask.mgz. Hope that's correct... > > Thanks, > > Torsten > > On Tue, 2011-10-04 at 09:07 -0400, Bruce Fischl wrote: >> and which volume are you editing? >> On Tue, 4 Oct 2011, Torsten Ruest wrote: >> >>> Hi Bruce, >>> >>> thanks for your quick reply. No I am editing using the following >>> command: >>> >>> tkmedit PARTICIPANT_FOLDER wm.mgz rh.white -aux brainmask.mgz >>> -aux-surface lh.white >>> >>> Thanks, >>> >>> Torsten >>> >>> On Mon, 2011-10-03 at 11:22 -0400, Bruce Fischl wrote: what pial edits to you want to undo specifically? Was it just edits to the brain.finalsurfs.mgz volume? On Mon, 3 Oct 2011, Torsten Ruest wrote: > Hi there, > > I think there is an option to remove all edits that have been > incorporated using recon2 -clean. > > Is there a chance that I can selectively undo all incorporated pial > edits (ie that have been incorporated by running "recon-all -subject > TEST -autorecon2 > TEST-2.log")? > > Thanks very much in advance, > > Torsten > > > > ___ > 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
Re: [Freesurfer] tkmedit window size
Hi Torsten, I believe we have this on our to do list for tkmedit fixes. Allison On Tue, 4 Oct 2011, Torsten Ruest wrote: > Hi there, > > I was wondering whether there is better option to resize the tkmedit > window: when I drag it bigger, it appears that the same change in aspect > ratio is applied to the image I am working on. When using the zoom > option (x2), the image I am working on doesn't fit completely into the > window anymore, while x1 is too small. Ideally I'd like to drag the > window bigger while leaving the image untouched, followed by zooming > into to make the image bigger. Is this possible? > > Thanks very much in advance, > > Torsten > > ___ > 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] (no subject)
Hi Heather, The cerebellum is not included in 5.1's total subcortical gm or total gm volumes. Let me double check on what is included in the subcortical gray matter total volume. Allison On Mon, 3 Oct 2011, Lugar, Heather wrote: > Can you please tell me if the cerebellum is included in Freesurfer 5.1's > total subcortical gray and/or total gray matter volumes? Also, what exactly > is included in the total subcortical gray (everything that's produced in the > aseg volumes)? > > Thanks so much, > Heather > ___ > 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] Incorrect pial surface
Okay, I'll take a look. Allison On Mon, 17 Oct 2011, Jordan Pierce wrote: We've uploaded the file as 30193retry.tar.gz Jordan Pierce ___ ___ 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] "psubmit: Command not found" error
It would be pbsubmit and would only work if you are logged into seychelles. On Thu, 2 Oct 2008, Jared Price wrote: Hi everybody, this is Jared over at the Brigham. Quick question for anyone who knows. I am trying to rebuild a subcortical atlas using the script rebuild_gca_atlas.csh. When calling the script I almost immediately get the error "psubmit: Command not found." I would like to get this working before I leave work today, so if anyone knows something about this error please let me know as soon as possible. ___ 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
Re: [Freesurfer] brainmask.mgz
It's the volume created after the first normalization and skull stripping. Allison On Wed, 12 Nov 2008, Alexa Nardelli wrote: Hey, I was just wondering if the brainmask.mgz file is the image after normalization? Thanks Alexa ___ 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
Re: [Freesurfer] recon-all rerun
recon-all will copy the brainmask.auto.mgz to the brainmask.mgz so they should be the same. Allison On Tue, 2 Dec 2008, Barkay, Gavriel wrote: Hi, I ran recon-all -all crashed for reasons unrelated to FreeSurfer. I re-ran the analysis without -clean. Is the new skull stripped volume stored in brainmask.auto.mgz instead of brainmask.mgz? Thanks, Gabi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: Res: [Freesurfer] Segmentation
Kelly, The aseg looks good to me (as far as just those two slices go - of course you would need to check every slice). I'm not sure I understand your question about separating them. As far as FreeSurfer's goal, this looks like a good result. Allison -- On Tue, 13 Jan 2009, Kelly Silva wrote: Hi, Bruce I´m sending some pictures of aseg.mgz. Is this well done? Is there any objective and specific criteria to separate the cerebelum from the cortex? Is really necessary to do the manual segmentation on that area? Thanks, Kelly De: Bruce Fischl Para: Kelly Silva Cc: freesurfer Enviadas: Segunda-feira, 12 de Janeiro de 2009 15:40:34 Assunto: Re: [Freesurfer] Segmentation Hi Kelly, did you check the aseg.mgz? Did it separate them properly? cheers, Bruce On Mon, 12 Jan 2009, Kelly Silva wrote: Hello, I´m sending an image and I want to know how is the best way to separate cerebelum from the cortex with the preservation of the both structures. Thanks! Best regards, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com Veja quais são os assuntos do momento no Yahoo! + Buscados: Top 10 - Celebridades - Música - Esportes Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Doubt pial segmentation
You do not need to manually separate the cerebellum from the cortex if the pial surface is accurately following the cortex (as it's doing in the pictures you sent). In fact, deleting too much cerebellum might cause other problems. Do you have any other reason why you want to separate them? Allison -- On Wed, 14 Jan 2009, Kelly Silva wrote: Hello, Thanks por the answers! Now I´m sending 3 images: 1) no segmentation, 2) segmentation with separation of cortex and cerebellum with radius 1, 3) segmentation with separation of cortex and cerebellum with radius 2. Wich image is the best way and use of radius to separate cerebellum from cortex? Thanks, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Mean Curv
The mean curvature for that particular parcellation. There is a slide demonstrating curvature here: https://surfer.nmr.mgh.harvard.edu/fswiki/ArticlesSlidesAndPosters Under the Slides section, the one called "Anatomical Analysis with FreeSurfer". It's slide #14. -- On Tue, 27 Jan 2009, Vina Goghari wrote: Hello all, What is the mean curv in the stats files a measure of? Thanks kindly, Vina ___ 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
Re: [Freesurfer] Doubt manual segmentation
Kelly, For your first question, how are you erasing it? The only way to change the label of a voxel in the segmentation is to call it another label - there is no real "erase" option as there are with white matter edits. If you want to change the label of the voxel, you will need to choose another label to call that voxel from the list of structures. I would suggest downloading at least the aparcstats2table fix because it will be important if you have any missing values. If it's no trouble, might as well download all of them to avoid any future problems but if you're sure you won't run into those problems, you don't have to. Allison On Mon, 23 Feb 2009, Kelly Silva wrote: Hello, 1) We have done the manual segmentation of one subcortical structure and we have observed that when we erase some area, it appears "none" in the "sgmtn label" from tkmedit window. Is there any problem whit this? 2) When we install the new version of freesurfer (4.2), is it necessary to put the fixes that appears on the freesurfer web? Thanks and best regards, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] about segmentation
I will edit the wiki page - I believe it is wrong. You cannot erase a segmentation by using the 3rd mouse button. In order to erase, you actually have to re-draw what the underlying segmentation was originally. If you are working on the aseg.mgz and plan to save your edits as aseg.mgz, to "erase" something you adding in error you right click on the Edit Segmentation button and the Segmentation Brush Info window will pop up. From the list of structures, choose the one that the area you edited was originally. For example, if you were adding thalamus on top of Left Cerebral White Matter and what to delete the thalamus label, choose Left Cerebral White Matter and use the 2nd mouse button to draw over the thalamus voxels you want to remove. If you are creating a segmentation and not saving it as aseg.mgz, you probably want to choose "0 Unknown" from the Segmentation Brush Info list to "erase" segmentation you have added. Allison -- On Fri, 20 Feb 2009, Bruce Fischl wrote: when you erase them they probably show the underlying gray-scale of whatever volume you are showing On Fri, 20 Feb 2009, Silvia biopanda wrote: Thanks Sita for your anwser, but, i'm sure that i'm using the correct tool, the thing is that i can erase the wrong voxels, but, when i erase them, they get coloured with a diferent contrast, i have tried to change the volume tool configuration and still appears with different contrast (a grey colour) thanks Silvia 2009/2/19 Sita Kakunoori : Make sure you are selecting the 'Edit segmentation tool' on the tkmedit tools window. You can also press the 'g' key to select the tool. Sita. On Thu, 19 Feb 2009, Silvia biopanda wrote: Hi, we are making changes in the aseg.mgz and we need to know how to erase a wrong pixels. we read in the tutorial that the button three erases, but it doesn't work.how can we do? cheers, SK ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] t4_read error
This message appears in the recon-all.log for several data sets I have here and all that data looks good. The most important thing is how your data looks. Does it look okay? I'm not sure why this message is there (Nick?) but I think you can ignore it. Allison On Sat, 18 Apr 2009, Zhen Zonglei wrote: The log files from both version 4.03 and version 4.30 report this error( t4_read: talsrcimg_to_711-2C_as_mni_average_305_t4 read error ). It occurs in imgreg_4dfp. attachment is my logfile,please check it. 2009/4/17 Allison Stevens What version of FreeSurfer are you using and what step of the process does that error appear in? Allison -- On Fri, 17 Apr 2009, Zhen Zonglei wrote: Dear all: Recon-all has finished without error in my reconstruction. However, when I checked recon-all.log, I found three was a error ?t4_read: talsrcimg_to_711-2C_as_mni_average_305_t4 read error?. What?s this error mean? Does it have some effects on my reconstruction? Thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] (no subject)
recon-all -all will take approximately 30 hours. It depends on the quality of your data and how many errors need to be fixed. Allison -- On Wed, 29 Apr 2009, Elina Pitri wrote: Hello Freesurfer Creators, I am wondering how much time should Volume and Surface processing (using recon-all commands) take. thanks, Elina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] mri_fill
The page up and page down buttons scroll through slices in both tools. If you have any problems or requests please let me know. We have abandoned scuba and probably will not be offering any support for it, however freeview is still in development. Allison -- On Tue, 19 May 2009, Falk Lüsebrink wrote: Hi Allison and Nick, Thanks for the info. The wiki didn't mention that either freeview or scuba (dev only) would be available in the current release. I tried both scuba and freeview and I'm wondering if there is some easy way to browse through the slices from either the sagital, coronal or axial view. Using scuba I could enter the RAS or index coords or is there something else I'm missing? In freeview I think I have to switch between the navigation tool and voxel edit tool or is there another way? At first glance freeview does appeal more to me in terms of simply erasing some voxels, so I think I will stick with it. Thanks in advance, Regards, Falk -Original Message- From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu] Sent: Tuesday, May 19, 2009 5:38 PM To: Nick Schmansky Cc: Falk Lüsebrink Subject: RE: [Freesurfer] mri_fill Falk, I can help you get started with scuba or freeview. For freeview, you type: freeview -v volume.mgz and it will load your volume. There is a help guide in there to take you through all the tools. Let me know if you need any help. Allison ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] brainmask.mgz recan-all and nu_correct error
Iwo, If you do ls $FREESURFER_HOME/bin Do you see mri_nu_correct.mni there? If you do, this message might help you: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06793.html Essentially, you have to make sure the nu_correct uses perl so you need to make sure it knows where it's located. If you don't have that binary, then you'll need to download it. Let us know, Allison -- On Fri, 29 May 2009, Iwo Bohr wrote: Hello everybody, Since I was corresponding with a few persons separetly, it required resending the same information to all of them. So I am getting back to the general forum with my still unsolved problem. To recap: when I run recaon-all pipeline as below: [iwob...@huxley FMRI]$ recon-all -autorecon1 -i NCVI-JR001TH_T1WIR_brain-conv.nii.gz -subjid test -all -force (with -autorecon1 option or without, similar situation occurs with -make option) It fails to output many necessary files, including brainmask.mgz, and the error message upon the completion of the pipeline is as follows: ERROR: nu_correct recon-all exited with ERRORS at Thu May 28 12:06:45 BST 2009 I attach a more detailed log file. I hope that now somebody will be able to help me :) Many thanks in advance, Iwo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] A question about cortical foldings
You can find this information in: /stats/?h.aparc.stats Allison -- On Fri, 29 May 2009, Zhangyuanchao wrote: Dear Mr or Ms Is there any way that we can obtain curvature value of the pial surface? I am not sure whether lh.curv is the curvature file that I want. How can I calculate the mean curvature, Gauss curvature of the pial surface and the GM/WM interface? Is there any built-in function in freesurfer to calculate the above index? Is there any other measures of cortical foldings in freesurfer besides lGI and curvature? Thanks a lot! yczhang ___ ÿÿ http://card.mail.cn.yahoo.com/___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] remove random factor
Dana, I believe you can achieve this by running recon-all on the subjects with the -norandomness flag. Unless you are using a version of FreeSurfer that is older than v3.0.4 - let me know if you are. -- On Mon, 15 Jun 2009, Dana W. Moore wrote: Hi all, I have run the same image twice with recon-all and gotten different results for the cortical parcellation, with regions of the cortex differing an average of 2% in volume and the biggest difference being 11% (left bankssts). This is on a healthy, elderly brain. I'd like to try running images removing the random factor that apparently causes these differences. I found instructions on the internet to create an expert-options file to remove this random factor. I was wondering where this file should be saved. My problem is I am actually working remotely with parallel processing nodes, and I don't have permission to write to the freesurfer home directory. I was wondering, if I could use the whole path when I enter this command into recon-all, and then save it anywhere I like. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2...@med.cornell.edu ___ 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
Re: [Freesurfer] FW: qdec- aparc.a2005s.thickness
Hi, This is a bug in an older version of FreeSurfer. What version are you using? Can you upgrade to a newer version? Allison -- On Tue, 16 Jun 2009, Sharmili 57 wrote: hey, Loading aparc.a2005s.thickness i get the attached error message. Does anybody know how to solve this problem? Posteingang immer voll? Der erste Speicher, der mitwächst: Unbegrenzter Speicher bei Windows Live Hotmail! _ http://redirect.gimas.net/?n=M0906xFTP_SpringCampaign2 --> Für Fotos hier abdrücken <-___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Qdec
Antonio, Can you describe what qdec is showing that's wrong or send a screenshot of it? Thanks, Allison -- On Thu, 18 Jun 2009, free_sur...@virgilio.it wrote: Dear Freesurfer users, We are experiencing a problem using Qdec (FS version 4.2.0; Qdec 1.0) for group data analysis. Indeed, the qdec display [after creating the qdec.table.dat and the .levels files] doesn't visualize properly (as in the tutorial) the Data Table View and other window-options that should allow us to select "Generate Stats Data Table" and proceed with the group analysis. Any suggestion would be greatly appreciated. Many Thanks in advance for your help, Antonio Gallo, MD, PhD Department of Neuroscience Second University of Naples Ph: +39-081-5665090 ___ 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
Re: [Freesurfer] longitudinal stream command line arguments
I looked at the revision history of the wiki and it shows a change to "-tp" so I believe that is the correct one to use. However, I was able to run both versions without error. When Nick returns, he can confirm but I think you should be fine using -tp. Allison -- On Fri, 19 Jun 2009, Dabbs (Kevin) wrote: The command line arguments for creating the base subject in Freesurfer Ver. 4.4 longitudinal stream do not agree between the Wiki and recon-all --help. On the Wiki support page, 2. create the base template and process it cross sectionally: recon-all -base -tp -tp ... -all From recon-all --help 2) create base subject and cross-sectionally process: recon-all -base longbase -base-tp tp1 -base-tp tp2 -all Is the correct argument "-tp" or is it "-base-tp" Thanks for the software and support, Kevin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Where can I read the manual for old freesurfer version (some new information)
Sure. Since that release was on 11-25-06, I will send you the last edited version of that page before that date (on 8-22-06) unless I find the latest version without all the changes. Allison -- On Mon, 29 Jun 2009, Bruce Fischl wrote: I'm not sure we have it so easily. Does anyone know? On Mon, 29 Jun 2009, Zhang, Xiaochu (NIH/NIDA) [F] wrote: The freesurfer I am using now is this version, "freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.4". I knew there is much improved in the current version.However, I have about 80 participants done in this old version. I only want to add several new participants and do some group anlaysis. Today I read the wiki and found a lot of things in "GroupAnalysis" have been changed. I tried to follow the new workflows but I found it is not suit to old verison. Who can do me a favor and give me the manual for the old version? My advisor asked me for result just now. Thank you so much! Xiaochu Zhang PhD Visiting Research Fellow Neuroimaging Research Branch National Institute on Drug Abuse - IRP Biomedical Research Center 251 Bayview Blvd. Suite 200 (NIDA) Baltimore MD 21224 Tel: 443-740-2619 ___ 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
Re: [Freesurfer] Error message starting qdec analysis
Rosa, I'm not sure, but the last time someone wrote about this error message, the problem was that they had more than 2 levels for one of their factors. By any chance, did you have more than two for the factor you included in these designs? -- On Mon, 6 Jul 2009, Rosa Steimke wrote: HI! When I sart the qdec analysis an error message comes up at around 70%. The error message says: Error in Analyze: command failed: mri_glmfit ÿÿy/Users/.../qdec/alh/y.mgh ÿÿfsgd /Users/.../qdec/alh/qdec.fsgd dods ÿÿglmdir /Users/.../qdec/alh ÿÿsurf fsaverafe lh ÿÿlabel /Users/.../fsaverage/label/lh.cortex.label In my terminal window the last thing it says is Reading in average area /Users/steimke/Rosa_MRTs/fsaverage/surf/lh.white.avg.area.mgh ERROR: no contrasts specified Do you know what the problem is? Thanks in advance! Rosa Steimke Rosa Steimke Student Master of Neuroscience Vrije Universiteit Amsterdam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] qdec question
The newest version of FreeSurfer does not contain any changes to qdec I believe. Allison -- On Thu, 9 Jul 2009, Prapti Gautam wrote: Dear Freesurfers, I just have some quick questions regarding qdec: 1. How many covariates does the latest version of qdec allow you to select? I am using FS version 4.3.0 and I cannot select more than 2 continuous variables. I am just wondering if a newer version allows you to select more covariates. 2. Does qdec allow you to choose between study designs DOSS and DODS? I currently do not see this option and I think my current version of qdec defaults to the DODS option. Thank you for your time, Prapti ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] pial surface edits
What areas are these where the pial is not extended enough? In general, the pial surface might extend further if the white surface is extended further but you would only want to do that if wm was also being left out of the white surface. On Tue, 14 Jul 2009, Devdutta W wrote: Hi,I have been trying to figure out how to get freesurfer to select more of the grey matter than it does after running recon-all with autorecon2 option. I feel that there are portions of the grey matter in some of our images that are not being selected as indicated by the red outline of the pial matter. Is it possible to do that? I appreciate any help in this matter. Regards, Devdutta ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] window refresh problem with freesurfer v4.4.0
Are you opening them from the same terminal window? If so, one is running in the background and so you will not be able to use it. Open each from a different terminal window. -- On Wed, 15 Jul 2009 yzha...@artsci.wustl.edu wrote: Whenever i try to open two windows(ie.' tkmedit bert orig.mgz 'and' tksurfer bert rh pial') the original one will not respond or refresh unless i close the second one,even i turn on the redraw button in the tksurfer. Also,i put the two windows side by side and did not overlay them. i've tried a few combinations, ie. two tkmedit windows, one tkmedit one tksurfer, etc. all of them have the same problem. any idea what's going on? thanks a lot Yuning Zhang 4525 scott ave, medical school,Washington University in St.Louis,63110 Phone:314-362-1219 ___ 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
Re: [Freesurfer] (no subject)
The parcellation is created using the surfaces and a cortical atlas so you shouldn't have to worry about the subcortical segmentation overlabeling like that. Take a look at the aparc+aseg.mgz in tkmedit. -- On Fri, 4 Sep 2009, Kim, Miyoung wrote: > Hi. > > Just a quick question - is cortical parcellation performed based on the pial > line (red line) or the cortical segmentation (brown shade)? The reason for > this question is that after recon2 we have an area in the lower occipital > cortical region that is shaded as "cerebellum" (see attached) although the > pial line seems to have correctly outlined it. Is this a potential problem > that we need to fix and if so what should we do? Thanks for your help in > advance! > > > Miyoung > > > > This message contains confidential information and is intended only for the > individual named. If you are not the named addressee you should not > disseminate, distribute or copy this e-mail. Please notify the sender > immediately by e-mail if you have received this e-mail by mistake and delete > this e-mail from your system. E-mail transmission cannot be guaranteed to be > secure or error-free as information could be intercepted, corrupted, lost, > destroyed, arrive late or incomplete, or contain viruses. The sender > therefore does not accept liability for any errors or omissions in the > contents of this message, which arise as a result of e-mail transmission. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Finishing WMParc
You only need to use the flag -wmparc. Allison -- On Fri, 2 Oct 2009, Andrew Jahn wrote: > Hello, > > I recently ran a batch file on several subjects, but set a time limit which > prevented some of them from finishing all the steps of recon-all. In the > recon-all-status.log for some of them, the last line is "WMParc". I was > unable to find which option of recon-all would do only this step; should I > just rerun them with autorecon3? > > Thanks, > > -Andy > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit File menu option in gray...
If they are gray, it means you have not made any edits to the main volume yet (so there is nothing to be saved). The main volume is whichever volume you loaded into tkmedit first. If you made edits to the second volume (the aux volume), you have to save those changes by choosing "Save Aux Volume". -- On Wed, 4 Nov 2009, Gonzalo Rojas wrote: > Hi: > > Why the options "Save Manin Volume" and "Save Main Volume as" in > TkMedit' "File" menu appears in gray (disabled) ?... > > Sincerely, > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] pial error...
It is difficult to tell from one slice and one view what is going on but in general you can only get the pial boundary to extend more by extending the wm boundary (but of course, only where there is actual wm). The pial boundary grows out from the wm boundary so if the wm boundary is incorrect, the pial boundary may also be. From this one slice, that doesn't look like the problem but perhaps if you look at other slices, that could be an issue. If the pial boundary is correct in all other slices surrounding this one, then it is probably not a problem. -- On Wed, 4 Nov 2009, Gonzalo Rojas wrote: > Hi: > > How can I correct a pial boundary error such as that appears in the image > ?... > > Sincerely, > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error: could not read header information from T1 or orig
It usually says that if your SUBJECTS_DIR is not set to the correct location. Try doing: echo $SUBJECTS_DIR and see if it is the path to where your data is located. Allison -- On Tue, 10 Nov 2009, nluc...@artsci.wustl.edu wrote: > I have recently (in the past week) started receiving the following error > when trying to load in a single subject's inflated surface using tksurfer > lh inflated > > ERROR: could not read header info from T1 or orig in > > I have tried using a different T1 or orig file, but nothing seems to work. > Thoughts? > > Thanks, > Nate > > ___ > 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
Re: [Freesurfer] white matter edits
It's a little bumpier than usual but ultimately you would have to look at the surfaces in tkmedit to determine whether these are errors. Allison -- On Fri, 4 Dec 2009, Jesse Bledsoe wrote: > Hi experts, > > Should I be concerned about the number of white matter errors in the > attached tif? Is it normal or unusual to have this many white matter errors > after reconstruction? It seems like discussions on editing white matter > suggest there are usually only a handful, if any errors to the wm.mgz. > > Thanks so much, > > Jesse > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Registration for Upcoming Freesurfer Course now open, Feb. 1 & 2
Hello, The Freesurfer group will be offering a two-day Freesurfer Tutorial and Workshop on February 1st and 2nd at the Martinos Center in Charlestown, MA. A description of the February course and a list of the topics covered can be found on the Course wiki page here: http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription On that website, you will find a link to register for the course. There is only room for 28 total participants and registration is on a first-come, first-serve basis. Shortly after all spots are filled, information will be sent out about hotels and parking. If you would like to arrange those details now, you can find all the information that will be sent out on the Course wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription THINGS TO KNOW BEFORE YOU REGISTER: 1. The registration AND payment deadline is January 8, 2010. 2. fMRI analysis is not a component that is taught in this course. 3. Payment can only be done in the form of a check or if you are from within the Partners network, a fund transfer can be arranged. Credit Cards are *not* accepted. 4. There are no refunds if you cannot attend the course. You can put the tuition payment towards the next course or send someone else in your spot. 5. All questions about payment should go to Stacey Ladieu (slad...@nmr.mgh.harvard.edu). Before e-mailing Stacey, please read the Course wiki page (listed above) and the registration page, carefully. Most questions participants have are answered there. 6. If the course is full, please register to be placed on the waiting list *only* if you think you could attend the course on short notice if a spot were to open up. Regards, The FreeSurfer Team ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mris_volmask ERROR
Guang, Without seeing the recon-all logs, I'm not exactly sure what happened but running "recon-all -s" wouldn't have finished running the processing stream so you would be comparing unfinished data to finished data. -- On Tue, 8 Dec 2009, Guang Zeng wrote: > > Hi, there, > > I submit several subjects to FS piepline using our Sun Grid Engine System, > all of them failed at the same place which is > the mris_volmask step in autorecon3. It gave me an error like: > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line > 372 > vtkMultiThreader (0x33d05a90): Unable to create a thread. pthread_create() > returned 12 > > I > knew this error is caused by some VTK function FS used to allocate > memory. So what I did is I use recon-all -s subjectid , and the process > will finish. > > What happen is the same subjects have been run on our local machines, and > finished without any problems. > However, when I looked at the wmparc.stats file of the same subject, the > results are quite different. > > For example, > ctx_isthumus cingluate and ctx_posterior singulate value are not zeros for my > local machine results, while > ctx_isthumus cingluate and ctx_posterior singulate value are zerosfor > my SGE machine results. > > And this problem have to all these subjects. Another funny thing is if I > look at the ?h.aparc.stats file, the results from SGE and local machine are > the same, while > when I load the results to tksurfer, they are quite different. > > So my question is: > > Since I need use SGE to run multiple subjects again, next time when I met > this mris_volmask ERROR, I need rerun the process from the beginning, not > from autorecon3, right? > > Thank! > Guang > > _ > Chat with Messenger straight from your Hotmail inbox. > http://www.microsoft.com/windows/windowslive/hotmail_bl1/hotmail_bl1.aspx?ocid=PID23879::T:WLMTAGL:ON:WL:en-ww:WM_IMHM_4:092009 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] correction of pial surface...
It looks like there might be some wm that is not labeled as wm. If you fix this first (by adding wm to the wm.mgz or adding control points if it is an intensity problem), that should fix the pial surface. -- On Wed, 24 Feb 2010, Gonzalo Rojas wrote: > Hi: > > How can I correct the pial surface in the image that I am sending attached > ?... > > Sincerely, > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] correction of pial surface...
Gonzalo, It's difficult to tell on just this one slice and I'm more used to viewing scans in the coronal plane. If you turn the aseg.mgz on, is that part of the subcortical gm? If not and you believe it to be cortical gm, let me know and we'll take a look. Allison -- On Wed, 24 Feb 2010, Gonzalo Rojas wrote: Hi: Thanks you very much for your answer... I think that wm not labeled as wm is the problem shown in arrow 1... but how can I fix the problem of arrow 2 ?... Sincerely, Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl El 24-02-2010 14:55, Allison Stevens escribió: It looks like there might be some wm that is not labeled as wm. If you fix this first (by adding wm to the wm.mgz or adding control points if it is an intensity problem), that should fix the pial surface. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] problem on freesurfer
Xiaoying, You can find information about changing the skull strip thresholds on this wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix The wmparc.mgz has the wm parcellated and labeled according to the closest cortical (gm) region. The aparc+aseg.mgz will show you the gm regions as well as the wm regions. The difference between aparc+aseg.mgz and aparc.a2005s+aseg.mgz are that they use different atlases to determine how to parcellate the gm. Information about the differences between these two atlases can be found here: https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation and here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg09585.html Allison -- On Fri, 5 Mar 2010, Xiaoying Tang wrote: > Hi Bruce, > > Thanks a lot. > > I have finished the running of autorecon3. I got three new files: > aparc+aseg.mgz; aparc.a2005s+aseg.mgz;wmparc.mgz. What's the difference > between the first two files? Which corresponds to the grey matter? > > By the way, I failed when using autorecon1 to do skull stripping. Besides > manual correction, is there any other automatic way to correct the result(I > have tried to change the threshold value, not good result)? > > Looking forward to your early reply. > > Best, > Xiaoying > > - Original Message - > From: Bruce Fischl > Date: Friday, March 5, 2010 8:41 am > Subject: Re: [Freesurfer] problem on freesurfer > To: Xiaoying Tang > Cc: ni...@nmr.mgh.harvard.edu, Freesurfer@nmr.mgh.harvard.edu > > >> Hi Xiaoying, >> >> there are gray matter estimates in aseg.mgz, but you need to run >> autorecon3 to get the surfaces that let us estimate cortical gm most >> accurately. >> >> cheers, >> Bruce >> On Fri, 5 Mar 2010, Xiaoying Tang wrote: >> >>> Hi Nick, >>> >>> Sorry, I am not sure whether I can successfully post my problem on >> the mailing list. So I send you the email and cc it to the mailing list. >>> >>> I now have a problem on freesurfer. After run auto-recon2, I am >> supposed to get grey matter and white matter. The white matter is in >> the form of wm.mgz, but I can't find something like gm.mgz. Can you >> tell me where is the grey matter? Is it aseg.mgz? >>> >>> Looking forward to your early reply. >>> >>> Sincerely, >>> >>> Xiaoying >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> >>> >>> >>> >> >> >> 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 >> . 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.
Re: [Freesurfer] brainmask/wm edits
Hi Helen, That's a good question. You don't have to start at autorecon1, however. When you run -autorecon2-wm or -autorecon2-pial one of the first steps is: mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz which is changing the brain.finalsurfs.mgz to take into account the changes you made to the brainmask.mgz. Your edits are not lost. Allison -- On Thu, 11 Mar 2010, Helen Keefe wrote: > Hi, > > I have a similar questionto the one listed below. > After I edit brainmask.mgz and wm.mgz, my understanding was that I could > run > autorecon2-wm > > and would not have to run autorecon2-pial because -wm will run > everything else through the end of -autorecon2. > > However, if brainmask.mgz is run at the end of autorecon1, don't I need > to run autorecon1 again, since wm or contol point edits would alter the > brainmask?? > > Thanks for help, > Helen > > > > "Hi Dana, > > you can do autorecon2-cp and it will do both things (the wm comes after > it in the stream anyway) > > cheers > Bruce > On Tue, 9 Mar 2010, Dana W. Moore wrote: > >> Hello everyone, >> >> There is an image that needs white matter edits (editing voxels) as >> well as control points. I know the two commands I need to re-run are >> autorecon2-cp and autorecon2-wm. Can I do both kinds of edits and >> somehow combine the -cp and -wm commands, or do I need to do the >> control points first, re-run, and then do further white matter edits? >> >> Thanks, >> Dana >> > > > > ___ 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] Extracting ROIs from aparc.a2009s+aseg.mgz
Liang, mri_annotation2label will separate all the ROIs in the ?h.aparc.a2009s.annot - is this what you need? I'm not sure what you mean by "mask image based on this image using 1, 2". You can merge or split labels as well. To display aparc.a2009s+aseg.mgz in tkmedit, you can do: tkmedit subjid orig.mgz -segmentation aparc.a2005s+aseg.mgz Allison -- On Wed, 10 Mar 2010, liang wang wrote: > Hi FS experts, > > Does anyone know how to extract these ROIs (including all gyral and sulci) > from the image . I just want to create a mask image > based on this image by using 1, 2, .. to code different brain areas. Thanks > for your solutions. > > Also, I can not display the image using the following command: tkmedit > subjid orig -aux brain -aparc.a2009s+aseg.mgz, but can correctly display > . Any advise would be appreciated. > > Liang > > ___ 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] Extracting ROIs from aparc.a2009s+aseg.mgz
Liang, We have a very good tutorial which takes you through what you would like to do. It's located here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual There is also some information on registration here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalRegistration Having the aparc divided up isn't necessary to do them though. Allison -- On Thu, 11 Mar 2010, liang wang wrote: > Hi Allison, > > Thanks. I have used the command line below to separately create many label > files, each of which include vertex number and XYZ coordinates. > mri_annotation2label --subject BNC006 --hemi lh --labelbase aparc.a2009 > > Sorry for not declaring my intention previously. What I actually want to do > is utilizing the gray ROIs recorded in aparc.a2009s+aseg.mgz to generate the > average time courses of each ROI from BOLD fMRI scanned from the same > subject. Can you give some advice how to accurately make it. Also, I am > worried the registeration issues across different modality images. > > Best, > Liang > > 2010/3/11 Allison Stevens > >> Liang, >> mri_annotation2label will separate all the ROIs in the >> ?h.aparc.a2009s.annot - is this what you need? I'm not sure what you mean by >> "mask image based on this image using 1, 2". You can merge or split labels >> as well. >> >> To display aparc.a2009s+aseg.mgz in tkmedit, you can do: >> tkmedit subjid orig.mgz -segmentation aparc.a2005s+aseg.mgz >> >> Allison >> -- >> >> On Wed, 10 Mar 2010, liang wang wrote: >> >> Hi FS experts, >>> >>> Does anyone know how to extract these ROIs (including all gyral and sulci) >>> from the image . I just want to create a mask image >>> based on this image by using 1, 2, .. to code different brain areas. >>> Thanks >>> for your solutions. >>> >>> Also, I can not display the image using the following command: tkmedit >>> subjid orig -aux brain -aparc.a2009s+aseg.mgz, but can correctly display >>> . Any advise would be appreciated. >>> >>> Liang >>> >>> >>> >> >> 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
Re: [Freesurfer] problem on recon-all
Xiaoying, There are directions for how to do this located here: https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ?highlight=%28FAQ%29#SkullStrippingOptions Allison -- On Fri, 12 Mar 2010, Xiaoying Tang wrote: > Hi all, > > When we do recon-all, we usually do autorecon1, autorecon2, and autorecon3 in > sequence. But now suppose I have already have a very good skull-stripped > subject. I mean I don't need to do skull-stripping with freesurfer. But I > want to get greymatter and white matter, which are generated in autorecon2 > and autorecon3. Is there any way to do this? > > Looking forward to your early reply. > > Best, > Xiaoying > ___ > 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] Bad pial surface
Ed, Usually a problem with the pial surface indicates a problem with the white surface and fixing the wm.mgz will fix the pial. But you said the wm segmentation is okay in the areas where the pial is a problem? What area of the brain are you finding this problem? Allison -- On Fri, 12 Mar 2010, Ed Gronenschild wrote: > Hi, > > Reviewing the results of recon-all I noticed that > the segmentation of wm and gm was OK but that > the computed pial surface chopped away an > unacceptable amount of gm voxels, too many to > manually edit. Is there a way to cure this problem > by choosing some options? > I used version 4.5.0 on a Mac Intel. > > Ed > > ___ > 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] How to transform brain.mgz back to native space
Liang, You can find instructions on how to do this here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat Sometimes using mri_convert will cause the orientation to be off so you may want to follow those instructions instead. Allison -- On Sat, 13 Mar 2010, Bruce Fischl wrote: > Hi Liang, > > you should just be able to use the -rl (reslice like) option in > mri_convert and give the orig/001.mgz as the target. > > cheers > Bruce > > On Fri, 12 Mar 2010, liang > wang wrote: > >> Hi FS experts, >> >> I find that FS does make a great skullstrip and extract a perfect brain (ie. >> brain.mgz). I am thinking to register this brain to MNI152 standard space >> using FSL. Does anyone know how to transfer the brain (256.^3, 1mm ) to >> subject-specific native space (224*256*176, 1mm). Thanks in advance. >> >> Liang >> >> > ___ > 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] How to transform brain.mgz back to native space
I've also been trying to link these type of pages on here: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ -- On Tue, 16 Mar 2010, Bruce Fischl wrote: > Hi Liang, > > are you doing a "text" search on the wiki? Hopefully that would find it. The > "titles" search is useless. > > cheers, > Bruce > On Tue, 16 Mar 2010, liang wang wrote: > >> Hi Allison and Bruce, >> >> Thanks for your kind explanations and the website mentioned >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat. I am >> curious >> why I can not directly find this website from the main interface >> http://surfer.nmr.mgh.harvard.edu/fswiki. Is there a website listing all >> the >> great links. Thanks. >> >> Liang >> >> 2010/3/15 Allison Stevens >> >> > Liang, >> > You can find instructions on how to do this here: >> > http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat >> > >> > Sometimes using mri_convert will cause the orientation to be off so you >> > may >> > want to follow those instructions instead. >> > Allison >> > >> > -- >> > >> > On Sat, 13 Mar 2010, Bruce Fischl wrote: >> > >> > Hi Liang, >> > > >> > > you should just be able to use the -rl (reslice like) option in >> > > mri_convert and give the orig/001.mgz as the target. >> > > >> > > cheers >> > > Bruce >> > > >> > > On Fri, 12 Mar 2010, liang >> > > wang wrote: >> > > >> > > Hi FS experts, >> > > > >> > > > I find that FS does make a great skullstrip and extract a perfect >> > > > brain >> > > > (ie. >> > > > brain.mgz). I am thinking to register this brain to MNI152 standard >> > > > space >> > > > using FSL. Does anyone know how to transfer the brain (256.^3, 1mm ) >> > > > to >> > > > subject-specific native space (224*256*176, 1mm). Thanks in advance. >> > > > >> > > > Liang >> > > > >> > > > >> > > > ___ >> > > 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
Re: [Freesurfer] a question about wmparc.stats and aseg.stats
Guang, You'll want to use aseg.stats over wmparc.stats for those values. Allison -- On Tue, 16 Mar 2010, Guang Zeng wrote: > > Hi, there, > > I have a question about wmparc.stats and aseg.stats, > > In aseg.stats, I read, > > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume > Without Ventricles, 1132816.00, mm^3 > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, > 1156812, unitless > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1156812.00, > mm^3 > > In wmparc.stats, I read > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume > Without Ventricles, 206821.00, mm^3 > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, > 244540, unitless > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 244540.00, > mm^3 > > Why the BrainSegVolNotVent and BrainSegVol are so small in wmparc.stats? > Those values in wmparc.stats are the sum of what? > If I want to get the correct Brain Segmentation Volume Without Ventricles, > which value I should use? the one from wmparc.stats or the one from > aseg.stats? > > Thanks! > Guang > > > _ > Hotmail is redefining busy with tools for the New Busy. Get more from your > inbox. > http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:WL:en-US:WM_HMP:032010_2 ___ 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] Recon-All Talairach error
Dave, Yep, if it looks okay, just run with -notal-check. Allison -- On Wed, 17 Mar 2010, Dave Brohawn wrote: > Hello, > > I am working on unpacking a subject scanned in Bay 8 on Thursday, 3/11/2010. > > I entered recon-all -autorecon-all -s FB0011090A > > and after unpacking for approximately 45 minutes, it reported: > > > Wed Mar 17 12:52:07 EDT 2010 > talairach_avi done > # > #...@# Talairach Failure Detection Wed Mar 17 12:52:07 EDT 2010 > /autofs/space/seymour_001/users/folate_subjects/FB0011090A/mri > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > ***FAILED*** (p=0.0176, pval=0. < threshold=0.0050) > Linux seymour 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:20:55 EDT 2009 i686 > i686 i386 GNU/Linux > > recon-all exited with ERRORS at Wed Mar 17 12:52:07 EDT 2010 > > > Should I run without a talairach check if I manually look and it looks ok? > > Let me know, and thanks, > > Dave Brohawn > > > > FREESURFER_HOME: /usr/local/freesurfer/stable4 > > Build stamp: freesurfer-Linux-centos4-stable-v4.5.0-20100311 > > RedHat release: CentOS release 5.3 (Final) > > Kernel info: Linux 2.6.18-128.7.1.el5 i686 > > NMR Center info (/space/freesurfer exists): > > machine: seymour > > SUBJECTS_DIR: /space/seymour/1/users/folate_subjects/ > > PWD: /space/seymour/1/users/folate_subjects > > ssh seymour > setenv SUBJECTS_DIR /space/seymour/1/users/folate_subjects/ > cd /space/seymour/1/users/folate_subjects > > ___ > 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] recon-all failture
Try running this: recon-all -skullstrip -no-wsgcaatlas -s If that goes through without error, you can finish processing your data by running: recon-all -autorecon2 -autorecon3 -s Allison -- On Wed, 17 Mar 2010, Gabriel Go.Es. wrote: I was trying to run a recon-all and I recibe an error message, wich you can find attached (recon-all.log), it appears to be a rpoblem with the skull stripping (the watershed) i tryed the flag -nowatershed, but the recon does not work. what can i do??? any help will be so apreciated Best Regards Gabriel TEMPLATE DEFORMATION second estimation of the COG coord: x=127,y=105, z=104, r=9864 iterations GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=38 , nb = 22419 RIGHT_CERCSF_MIN=0, CSF_intensity=9, CSF_MAX=51 , nb = 1530 LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=45 , nb = 1332 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=35 , nb = 9837 LEFT_BRAINCSF_MIN=0, CSF_intensity=9, CSF_MAX=37 , nb = 9522 OTHER CSF_MIN=2, CSF_intensity=16, CSF_MAX=47 , nb = 198 mri_watershed Error: GLOBAL region of the brain empty ! Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Mar 15 09:45:02 CET 2010 _ Ahora Messenger en tu Blackberry® 8520 con Movistar por 0 ?. ¿A qué esperas? http://serviciosmoviles.es.msn.com/messenger/blackberry.aspx___ 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] drawing adjacent labels with shared boundaries, and labels near the edge of a patch
Lindsay, I think this wiki page might help: https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit Allison -- On Tue, 16 Mar 2010, Lindsay Lewis wrote: > hi, > > I am trying to manually draw a "grid" of many small ROIs/labels on an > occipital flattened surface patch in tksurfer, and am having 2 points > of confusion: > > (1) I want my labels to be directly adjacent to each other, but since > I am drawing manually, I am not sure how to use the boundary of one > label to define the boundary of the adjacent label? (obviously, > recreating the shared boundary manually each time will likely not be > exactly identical - there could be some voxels accidentally left out > between the two labels, or some voxels accidentally common to the two > labels) > > (2) I have some labels I want to extend all the way to the edge of the > patch. I keep doing my best to mark the vertex at the very edge, but > I keep ending up marking a vertex not all the way at the edge, or > slightly out in empty space beyond the patch. I am not sure how to > mark the very edge of the patch. > > If anyone has any advice regarding how to address these two issues, I > would very grateful! > > Many thanks. > ___ > 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] mri_surfcluster
Kelly, I believe they are in Talairach space. Information on how to get them in MNI space is located here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg10038.html Allison -- On Fri, 19 Mar 2010, Kelly Silva wrote: Hello, I would like to know if the output coordinates from the "mri_surfcluster" command is on the MNI space or on the Talairach. Thanks in advance. Best, Kelly Veja quais são os assuntos do momento no Yahoo! + Buscados: Top 10 - Celebridades - Música - Esportes Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com___ 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] the thickness of manually selected vertex
Guang, Working in tksurfer, be sure to first do to Edit > Deselect Label and Edit > Unmark all Vertices just to make sure nothing else is chosen besides the 4 vertices you are interested in (unless you are sure that's all you have clicked on). Then click on the 4 vertices you want to mark. After you have chosen the last one, go to Tools > Labels > New Label from Marked Vertices. Then File > Label > Save Selected Label naming it whatever you want with the .label extension. You can then run: mris_anatomical_stats -f blah.stats -l blah.label subjid lh changing the hemi to whichever one you made the label on. The resulting stats file should have 4 under NumVert otherwise it didn't work. Allison -- On Wed, 24 Mar 2010, Guang Zeng wrote: > > Hello, Bruce, > > Thanks a lot! > > I think my new question is how to save a label file of the 4 vertices I > selected. > > Thanks! > Guang > >> Date: Wed, 24 Mar 2010 16:15:35 -0400 >> From: fis...@nmr.mgh.harvard.edu >> To: freesurfer...@hotmail.com >> CC: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] the thickness of manually selected vertex >> >> Q1: yes. >> Q2: do you want each of them individually or the average? You can save a >> label file of the 4 vertices and use mris_anatomical_stats to get the >> average >> >> cheers >> Bruce >> >> On Wed, 24 Mar 2010, Guang Zeng wrote: >> >>> >>> Hi, there, >>> >>> I have two questions about the ?h.thickness file. >>> >>> If I load a subject's surface ?h.inflated using tksurfer, then I load its >>> thickness file ?h.thickness, >>> >>> By clicking mouse on the surface, I can read the corresponding curvature >>> value of a specific vertex. >>> >>> Q1, Here, the value next to 'Curvature' is actually its thickness value, >>> right? >>> Q2, If I select four vertexes on the surface, is there a way that I can >>> save the thickness values of these four vertexes into a txt file? >>> >>> >>> Thanks! >>> Guang >>> >>> _ >>> Hotmail is redefining busy with tools for the New Busy. Get more from your >>> inbox. >>> http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:WL:en-US:WM_HMP:032010_2 >> >> >> 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. >> > > _ > Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. > http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:WL:en-US:WM_HMP:032010_1 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Longitudinal processing edits
Ronald, This looks correct for now. I believe Martin is working on a way to make this easier for the future. Allison -- On Tue, 23 Mar 2010, Pierson, Ronald K wrote: > I apologize if this has been covered before, but I wanted to make sure I > understand the best way to edit at the appropriate times during the > longitudinal stream. > > > > 1) Run recon-all -all on each scan > > 2) If needed, control points are chosen on the individual scans, > and recon-all using the -cp option > > 3) Run the -base processing for the subject > > 4) WM and brain (pial) edits are done on the base, rerun as needed > > 5) Final longitudinal processing of each scan > > > > I assume the final processing of the individual scans should need very > little manual intervention, since the control points and edits will be > carried through to that stage. > > > > Is this correct, or have I oversimplified or missed something? > > > > Ronald Pierson > > Administrative Chair of Imaging, PREDICT-HD > Manager, Research and Development > Department of Psychiatry, Carver College of Medicine > W-278 GH, 200 Hawkins Dr > Iowa City, IA 52242 > > > > > > ___ 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 watershed threshold has no effect
Something like that I would say you usually have to manually edit. Allison -- On Fri, 26 Mar 2010, Andreas Berger wrote: > hello freesurfers, > > we are having a problem with insufficient skull stripping, in 66 out > of 200 subjects this affects the pial surface, as can be seen in the > attached screenshot1. since the problem is somewhat generalized in > location, i tried to change the watershed threshold as suggested by > the wiki. i tried the values 20, 15, 10, 5, 0 (recon-all -all -clean > -wsthresh n), but even 0 seems to have no effect (it looks different, > but not less skull), see screenshot2. am i doing it wrong? > ___ 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] Correcting subcortical segmentation
John, Information on editing the aseg is here: http://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations We generally advise against it if possible - what areas need editing? Allison -- On Thu, 1 Apr 2010, John Fredy wrote: > Hello all, > > I'm trying to obtain a set of statistics of subcortical segmentation from a > pacient with Huntington's disease. The tutorial of freesurfer shows six > possible case of error in freesurfer: correcting white/gray surfaces, > topological errors, skull removing, talairach transformation, among others. > But, how I can correct subcortical segmentation error? > > Thanks in advance > ___ 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] Recon-all problem (with talairach)
Janani, For the Failure Detection error, please take a look here: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.IgetanerrormessagefromtheTalairachFailureDetection.Whatdoesthismean.3F and http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07958.html For your other questions: 1) FreeSurfer can not work well on data with resolution bigger than 1.5mm^3. You need your input to have good wm/gm contrast in order for the surfaces to be created correctly. 2) I'm not sure what you mean by the first 50 files. In the series? I would imagine the name would matter. Allison -- On Tue, 30 Mar 2010, Janani Dhinakaran wrote: > I'm looking through it and also looking at tkregister2 help, and I have some > questions > 1)Does Recon only work on fully structural data? If you have funtional > information on it will recon fail? > 2)Also- Does it matter what the files are named... for ex- if the first 50 > are named JohnSmith_001_01_01.img and after that they are named > John^Smith_051_01_01.img... does it make a difference enough to fail recon? > > > On 30 March 2010 11:54, Martin Kavec wrote: > >> Hi Jan, >> >> the place to look at is >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach >> >> Best, >> >> Martin >> >> On Tuesday 30 March 2010 12:30:35 Janani Dhinakaran wrote: >>> Hello everyone, >>> I wanted to know what I can do to fix this error- it occurs when I'm >>> running recon-all -all -s Subject >>> >>> Tue Mar 30 11:27:20 BST 2010 >>> talairach_avi done >>> # >>> #...@# Talairach Failure Detection Tue Mar 30 11:27:20 BST 2010 >>> /home/s0964091/Desktop/Newdata/JS/mri >>> >>> talairach_afd -T 0.005 -xfm transforms/talairach.xfm >>> >>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >>> ***FAILED*** (p=0., pval=0. < threshold=0.0050) >>> Linux CRIC-0012 2.6.31-20-generic #58-Ubuntu SMP Fri Mar 12 04:38:19 UTC >>> 2010 x86_64 GNU/Linux >>> >>> recon-all exited with ERRORS at Tue Mar 30 11:27:20 BST 2010 >>> >>> Thank you for your help >>> Jan >> >> ___ >> 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
Re: [Freesurfer] Pial Surfaces Cutting off Gyri
Sherri, It's better if you compress the entire subject's directory and send that. In general, you can erase things from the pial surface but you can't add things to it. You can only get the pial surface to grow out more by changing the white surface (either through control points or adding voxels to the wm.mgz). -- On Wed, 7 Apr 2010, Sherri Novis wrote: > Thank you Bruce. I've had this prob randomly before - but recently it's been > each of the last 10 datasets - so I think its a process issue that I > introduced - but would love help from any direction. > > If I use the upload site - which files to you need? will send wm.mgz, > ?h.orig surface - any others? > > Thank you - > Sherri > > > > -Original Message- >> From: Bruce Fischl >> Sent: Apr 7, 2010 1:15 PM >> To: Sherri Novis >> Cc: Sita Kakunoori , freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Pial Surfaces Cutting off Gyri >> >> Hi Sherri, >> >> you may also have a topological defect near those control points, which >> is causing the surfaces to lose the wm (and hence the gm also). What does >> the wm.mgz look like there? Is the wm segmented correctly but not >> included in the ?h.orig surface? If you upload this data we can take a >> look, if you want. >> Bruce >> >> >> On Wed, 7 Apr 2010, Sherri Novis wrote: >> >>> Thanks Sita. I have struggled with how to capture very ghostly gray matter. >>> Sometimes throwing a CP in it works (I understand now this may be hosing >>> it sometimes) - if AR2-cp w/CPs in white matter is not driving the pial >>> surfaces to capture all the gray - is the only way to capture the ghostly >>> gray matter to directly edit the pial surface? >>> >>> I was trying to avoid that. I was told don't ever edit the pial surfaces - >>> not sure why though. Will manual edits of the pial surfaces cause other >>> problems in getting surface segmentation stats? >>> >>> Thank you - >>> Sherri >>> >>> -Original Message- From: Sita Kakunoori Sent: Apr 7, 2010 12:55 PM To: Sherri Novis Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Pial Surfaces Cutting off Gyri Hi Sherri, one of the control points seems to be in gray matter, which is probably causing this. Please try deleting it and rerunning autorecon2-cp. Sita. On Tue, 6 Apr 2010, Sherri Novis wrote: > Hello brilliant and generous FS people, > > I have introduced a problem I cannot solve. I am simply trying to > capture as much gray matter as possible. We have some very bad constrast > images (ghostly edeges where the gray matter should be). I'm adding > control points to try to capture - however, now when I run AR2-cp, the > pial surfaces go haywire on the superior borders of the slices. > > Attached are two images displaying the problem. > > I have edited wm.mgz to fill in the ventricles because I was getting > islands, and I manually edited the brainmask to remove some vasculature > that was being included in the pial surfaces. > > Can you tell me where I introduced this instability? > > Best Regards, > Sherri 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 > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problems segmenting monkey brain
Krishna, How have you processed this data? Have you used any of the suggested flags and/or parameters for monkeys? See: https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData -- On Wed, 7 Apr 2010, Srihasam, Krishna wrote: > Hi, > > I have a (0.35 mm)^3 resolution monkey brain which I am trying to segment. I > am unable to get the frontal cortex to segment properly. My WM.mgz looks good > ( I think), but after I do "recon-all -autorecon2-wm ", the surf that gets > created has no frontal cortex. I have attached two pictures of one slice, > with generated surface overlaid on WM.mgz ( WM_Surf133.jpg) and the same > generated surface on T1 image (NU-Surf133.jpg). I tried adding control > points, I manually edited the WM.mgz and nothing works. Any help will be > appreciated.. > > > regards, > Krishna Srihasam > Postdoctoral Fellow > Livingstone Lab > 220 Longwood Avenue, WAS 232 > Boston, MA 02115 > > ___ 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 watershed threshold has no effect
Thanks, Andreas. That clears it up. There was no attachment though. Can you send me the screenshots? -- On Tue, 13 Apr 2010, Andreas Berger wrote: > on one group of subjects i ran "recon-all -all -clean -wsthresh n", which > according to http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags > includes what "-clean-bm" does. > > on the other group i ran "recon-all -all -wshthresh n" after deleting > everything and converting them from raw invol data to freesurfer format > again. as i understand it, "-clean" is not required because no previous data > is there to be overwritten/cleaned. > > to prevent confusion, i am not comparing these two groups, it's just that we > have a separate group of subjects of which whe don't have the raw data, so i > had to use -clean. i compared using "-wsthresh" against not using it in a few > subjects from both groups. as far as the "-clean" flags are concerned, there > is no bug: they do change the result, so i assume the previous volume is > overwritten as it should, however the results are no improvement (see > screenshots). > > > > On Mon, 12 Apr 2010 15:54:47 -0400 (EDT) > Allison Stevens wrote: > >> Andreas, >> I'm not very clear on your response. Did using -clean-bm on the subjects >> you had used -clean on when running with -wsthresh, change the skull strip >> for the better? >> >> when you ran it on the already clean data set, you said using -wsthresh 0 >> still did not get a good skull strip? >> Allison >> >> -- >> >> On Fri, 9 Apr 2010, Andreas Berger wrote: >> >>> Sorry for the slow response, >>> >>> yes, the "-clean" flag should imply "-clean-bm" (among others) >>> >>> besides, on one group of the subjects i ran "recon-all -all -wsthresh n" >>> after converting them from invol data again, everything from scratch (no >>> cleaning required), with the same result. also, the fact that the surfaces >>> did change (however not as i hoped) indicates that it's not a problem with >>> the flags. >>> >>> >>> >>> >>> On Wed, 31 Mar 2010 13:01:32 -0400 (EDT) >>> Allison Stevens wrote: >>> >>>> Andreas, >>>> Did using -clean-bm work? >>>> Allison >>>> >>>> -- >>>> >>>> On Mon, 29 Mar 2010, Allison Stevens wrote: >>>> >>>>> Andreas, >>>>> Let me know how this turns out. The response you got about the command >>>>> (using >>>>> -clean-bm) is correct but since you used -clean, that should have worked >>>>> just >>>>> as well. Can you please let me know if using -clean-bm does anything >>>>> differently from -clean? If so, we'll have to investigate this as a >>>>> potential >>>>> bug. >>>>> Thanks, >>>>> Allison >>>>> >>>>> >>>> >>>> >>>> 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
Re: [Freesurfer] changing watershed threshold has no effect
Your surfaces look fine (at least in that slice). Why do you feel you need to strip away more skull? -- On Tue, 13 Apr 2010, Andreas Berger wrote: > thank you for replying, > > i reattached the screenshots. they were in my first mail but i think i broke > the thread by replying to the wrong adress once, sorry. screenshot 1 is > result of "recon-all -all", screenshot 2 is result of "recon-all -all > -wsthresh 0". what's weird is that next to the left hemisphere there's some > skull left that wasn't even there with default settings. > > EDIT: forgot to attach the screenshots, sorry once more... > > > On Tue, 13 Apr 2010 08:20:40 -0400 (EDT) > Allison Stevens wrote: > >> Thanks, Andreas. That clears it up. >> >> There was no attachment though. Can you send me the screenshots? >> >> -- >> >> On Tue, 13 Apr 2010, Andreas Berger wrote: >> >>> on one group of subjects i ran "recon-all -all -clean -wsthresh n", which >>> according to http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags >>> includes what "-clean-bm" does. >>> >>> on the other group i ran "recon-all -all -wshthresh n" after deleting >>> everything and converting them from raw invol data to freesurfer format >>> again. as i understand it, "-clean" is not required because no previous >>> data is there to be overwritten/cleaned. >>> >>> to prevent confusion, i am not comparing these two groups, it's just that >>> we have a separate group of subjects of which whe don't have the raw data, >>> so i had to use -clean. i compared using "-wsthresh" against not using it >>> in a few subjects from both groups. as far as the "-clean" flags are >>> concerned, there is no bug: they do change the result, so i assume the >>> previous volume is overwritten as it should, however the results are no >>> improvement (see screenshots). >>> >>> >>> >>> On Mon, 12 Apr 2010 15:54:47 -0400 (EDT) >>> Allison Stevens wrote: >>> >>>> Andreas, >>>> I'm not very clear on your response. Did using -clean-bm on the subjects >>>> you had used -clean on when running with -wsthresh, change the skull strip >>>> for the better? >>>> >>>> when you ran it on the already clean data set, you said using -wsthresh 0 >>>> still did not get a good skull strip? >>>> Allison >>>> >>>> -- >>>> >>>> On Fri, 9 Apr 2010, Andreas Berger wrote: >>>> >>>>> Sorry for the slow response, >>>>> >>>>> yes, the "-clean" flag should imply "-clean-bm" (among others) >>>>> >>>>> besides, on one group of the subjects i ran "recon-all -all -wsthresh n" >>>>> after converting them from invol data again, everything from scratch (no >>>>> cleaning required), with the same result. also, the fact that the >>>>> surfaces did change (however not as i hoped) indicates that it's not a >>>>> problem with the flags. >>>>> >>>>> >>>>> >>>>> >>>>> On Wed, 31 Mar 2010 13:01:32 -0400 (EDT) >>>>> Allison Stevens wrote: >>>>> >>>>>> Andreas, >>>>>> Did using -clean-bm work? >>>>>> Allison >>>>>> >>>>>> -- >>>>>> >>>>>> On Mon, 29 Mar 2010, Allison Stevens wrote: >>>>>> >>>>>>> Andreas, >>>>>>> Let me know how this turns out. The response you got about the command >>>>>>> (using >>>>>>> -clean-bm) is correct but since you used -clean, that should have >>>>>>> worked just >>>>>>> as well. Can you please let me know if using -clean-bm does anything >>>>>>> differently from -clean? If so, we'll have to investigate this as a >>>>>>> potential >>>>>>> bug. >>>>>>> Thanks, >>>>>>> Allison >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> 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
Re: [Freesurfer] Saving time in longitudinal processing
Jordan, The -subcortseg step is going to be looking for inputs that were created before it, so you can't really skip the steps before it. I suppose you can skip the surface steps afterwards as long as you understand that the aseg.mgz will not give you accurate wm and gm volumes. In order to get the volume stats, you need to run the -segstats step in -autorecon3. I'm not sure if you will get any complaints for missing files from not running the surfaces. I'm also not sure if there is anything in the longitudinal processing stream that would complain about this method - but hopefully Martin or Nick will chime in about that. Allison -- On Thu, 15 Apr 2010, Jordan Poppenk wrote: > Dear list, > > I am about to start processing a largish longitudinal dataset and wondered > whether I could save some processing time in the following ways: > > 1) I have seen written in a few places that only norm.mgz is used from the > cross-sectional stream during base template creation at the next stage. Does > that mean I can run "-autorecon1" only on each of the timepoints during the > cross-sectional processing stage rather than "-all"? > 2) As I am only interested in the subcortical output of the longitudinal > processing, can I include the flags "-autorecon1 -subcortseg" in all > remaining steps in the longitudinal stream to skip cortical processing, or > will that cause problems? > > Thanks for your help, > Jordan > ___ 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] Problem adding control points
Sasa, Are you middle clicking to add a control point? Allison -- On Tue, 27 Apr 2010, Sasa Kivisaari wrote: > Dear FreeSurfers, > > I'm a postgraduate student and recently started with FreeSurfer. I have > problems adding control points to the volumes I have loaded into tkmedit. For > some reason, after selecting the Edit Control Points -tool and clicking the > white matter voxels, I do not get the green crosses I should. Instead, I see > a red cross (the same I get when I choose e.g. the edit voxels tool), which > disappears after clicking another voxel. No control points are saved, > although I'm able to create the control.dat file. I'm running Freesurfer on > Mac Snow Leopard. > > Thank you for your help! > > Sincerely, > Sasa Kivisaari > ___ > 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] recon-all error autorecon3
There are a few suggestions for this from a previous question on the same matter. Please see here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07155.html Allison -- On Tue, 27 Apr 2010, Antoine Leflon wrote: > hi , > > I was processing autorecon3 and it screened me this error : > > #...@# Cortical ribbon mask Tue Apr 27 19:44:20 IST 2010 > /home/cami/freesurfer/subjects/ant/mri > > mris_volmask --label_left_white 2 --label_left_ribbon 3 > --label_right_white 41 --label_right_ribbon 42 --save_ribbon > --save_distance ant > > mris_volmask.bin: error while loading shared libraries: libtiff.so.3: > cannot open shared object file: No such file or directory > Linux pride 2.6.31-14-generic #48-Ubuntu SMP Fri Oct 16 14:04:26 UTC > 2009 i686 GNU/Linux > > recon-all exited with ERRORS at Tue Apr 27 19:44:20 IST 2010 > > __ > > Is it something important ? > > Antoine > > ___ > 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] fail to open .mgz data in tkmedit: DICOM image data in the sagittal view
Right, your command to see that file should be: tkmedit bai_hong_jun orig/001.mgz Also, it only did the first step because your command was: recon-all -i input -s subjid To run the entire processing stream, you'll want to do: recon-all -all -i input -s subjid Allison -- On Tue, 27 Apr 2010, Bruce Fischl wrote: Hi LJ, don't include the "mri" on the command line (it is assumed to be under mri) cheers Bruce On Tue, 27 Apr 2010, liyari5018 wrote: hi FS experts, FS can't recognize the file which was covert from a DICOM data in sagital view, here is an example of failure£º £¨see the annex for more detail £© r...@lijin-desktop:/usr/local/freesurfer/subjects/fuzhou_test# tkmedit bai_hong_jun mri/orig/001.mgz ERROR: cannot find /usr/local/freesurfer/subjects/fuzhou_test/bai_hong_jun/mri/mri/orig/001.mgz Error: Loading volume mri/orig/001.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. how can i do to solve this problem? thanks for your reply! LJ ___ 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] add the gray matter
Xin, You do not have to correct the pial surface for that area - these surfaces do not affect the aseg.mgz. You will often see the surfaces in the hippocampus/amygdala regions as inaccurate, however your aseg will look fine. Allison On Fri, 13 Jul 2007, Wang, Xin wrote: This is an example of my problem area (labeled with * in the fig). Do I need to correct the pial surface? If so, how to do it? Does this problem effect the values of hippocampus in the aseg.mgz? Many thanks, Xin From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 7/10/2007 10:39 AM To: Wang, Xin Cc: freesurfer Subject: RE: [Freesurfer] add the gray matter oh, I wouldn't worry about the surfaces in the hippocampus. They aren't meant to be accurate there. There is too much internal structure there - we model is separately in the aseg.mgz files. cheers, Bruc On Tue, 10 Jul 2007, Wang, Xin wrote: Dear, Dr. Fischl Thank you for your suggestion. My problems are around hippocampus. The grey/white surface is OK now. but some grey matters are not included in the pial surface. How to change the Pial surface? Thank you again, Xin From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Mon 7/9/2007 5:53 PM To: Wang, Xin Cc: freesurfer Subject: Re: [Freesurfer] add the gray matter it depends why it's not getting out far enough. Usually you need to add control points in the nearby white matter that are <110 on the brainmask.mgz volume. On Mon, 9 Jul 2007, Wang, Xin wrote: Hello, Group I need to edit the pial surface. I learned to remove points with tkmedit from the tutorial. But how to add gray matter in the pial surface? Thank you in advance. Xin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ReconAllDevTable
Thanks, Mike. I'll work on this. Allison On Fri, 2 Nov 2007, Michael Harms wrote: Hello, Just a couple miscellaneous items/suggestions regarding the very helpful ReconAllDevTable: 1) The entry for -inflate2 currently indicates that ?h.white is the input file. This should be ?h.smoothwm instead. 2) It might be helpful to add a line to the -skullstrip stage indicating the 'mri_em_register' command that preceeds 'mri_watershed' so as to indicate where the "talairach_with_skull.lta" file comes from that is used as part of 'mri_watershed' in v4.0.1 3) Do you have "archived" versions of the ReconAll table that are appropriate for previous stable releases? If so, it would be great if the wiki contained links to those. If not, it might be helpful to create such "snapshots" of the ReconAll flow table so that there is a convenient place to access the process flow that is most accurate for previous (non-developmental) releases. cheers, Mike H. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] checking problems
The tutorial is here (it's 2 pages, be sure to click 'next'): https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData Allison On Wed, 2 Jan 2008, Bruce Fischl wrote: Hi, we don't usually stop and check anymore as things fail pretty rarely. You can look at the tutorial on the wiki for examples of the types of failures and how to fix them. cheers, Bruce On Wed, 2 Jan 2008, Feng-Xian Yan wrote: Hi, I have some confusion. When I completely run the command, recon-all ¡Vs x249 ¡Vautorecon1, and I should stop to check for problems with intensity normalization, talairach transformation and skull stripping. How can I do to check these problems? And, which is I must do first? Thanks. ___ 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
Re: [Freesurfer] what is the prerequisite of cc in cortparc?
Kristine, You should be able to use -ccseg which occurs after the aseg is created in -autorecon2. First, you will need to copy your aseg.mgz to aseg.auto.mgz as this is the file that -ccseg will work on (in the dev version of FS, it uses the aseg.mgz). Allison On Tue, 22 Jan 2008 [EMAIL PROTECTED] wrote: Thanks! The MRI_cc works fine. It's just that I want to use the entire wmparc, and I worry that it may be skewed when the cc is not in there. The cingulate parcellations look a little off. Do you think there's any step in -autorecon2 (before -cortribbon) after the aseg I might try to start reprocessing to fix this? Best, Kristine Hi Kristine, you can just run mri_cc directly if you want: mri_cc -o aseg_with_cc.mgz $subject cheers, Bruce On Tue, 22 Jan 2008 [EMAIL PROTECTED] wrote: Hi I have a dataset originally processed with the Autumn 2005 FS version (2.2?). I know need wm segs, and in order to get this, I've tried to run -cortribbon -cortparc -cortparc2 -aparc2aseg -wmparc But the cc doesn't get labeled in the cortparc, and consequently (?) not in the wmparc either. I've also tried to rerun all of -autorecon3, but w/o difference. When rerunning recon-all -all, it gets fixed, but I would like to keep as much as possible as is, since I did lots of edits due to a temporal bias field problem. I've edited the asegs in some instances, and that is not kept by default. Grateful for tips on how far down in the processing stream I need to go to get correct wmparcs w/cc. Thanks, Kristine ___ 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
Re: [Freesurfer] what is the prerequisite of cc in cortparc?
That should be fine (-ccseg -cortribbon -cortparc -aparc2aseg -wmparc). Allison On Wed, 23 Jan 2008 [EMAIL PROTECTED] wrote: Thanks, I'll try that. Will I then need to redo all steps fromm -ccseg onwards if I want a correct wmparc at the end, or can I safely skip some? For instance, I could do -ccseg -cortribbon -cortparc -aparc2aseg -wmparc? Best, Kristine Kristine, You should be able to use -ccseg which occurs after the aseg is created in -autorecon2. First, you will need to copy your aseg.mgz to aseg.auto.mgz as this is the file that -ccseg will work on (in the dev version of FS, it uses the aseg.mgz). Allison On Tue, 22 Jan 2008 [EMAIL PROTECTED] wrote: Thanks! The MRI_cc works fine. It's just that I want to use the entire wmparc, and I worry that it may be skewed when the cc is not in there. The cingulate parcellations look a little off. Do you think there's any step in -autorecon2 (before -cortribbon) after the aseg I might try to start reprocessing to fix this? Best, Kristine Hi Kristine, you can just run mri_cc directly if you want: mri_cc -o aseg_with_cc.mgz $subject cheers, Bruce On Tue, 22 Jan 2008 [EMAIL PROTECTED] wrote: Hi I have a dataset originally processed with the Autumn 2005 FS version (2.2?). I know need wm segs, and in order to get this, I've tried to run -cortribbon -cortparc -cortparc2 -aparc2aseg -wmparc But the cc doesn't get labeled in the cortparc, and consequently (?) not in the wmparc either. I've also tried to rerun all of -autorecon3, but w/o difference. When rerunning recon-all -all, it gets fixed, but I would like to keep as much as possible as is, since I did lots of edits due to a temporal bias field problem. I've edited the asegs in some instances, and that is not kept by default. Grateful for tips on how far down in the processing stream I need to go to get correct wmparcs w/cc. Thanks, Kristine ___ 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
Re: [Freesurfer] Accidentally stopped during recon-all
You can do: "recon-all -make all -s and it will run all the remaining steps that have not been done or are out of date. On Fri, 25 Jan 2008, Chris Watson wrote: Hello, While running recon-all on a subject, my machine logged me off for an unrelated reason. It was stopped during -autorecon3, specifically at -surfreg (mris_register) for the right hemi. The left hemi was already done, I believe. What would be the command to start from that step, and continue to the end? Thanks, Chris ___ 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
Re: [Freesurfer] Accidentally stopped during recon-all
Oops, I should have asked what version you were using. The -make flag is not in v3. Instead you can do: recon-all -hemi rh -autorecon3 -nosphere -s This will run just the right hemisphere through the rest of -autorecon3. Doing -nosphere will skip the step before -surfreg which was already completed. Allison On Fri, 25 Jan 2008, Chris Watson wrote: Hi Allison, this is the error message I received: [EMAIL PROTECTED] subjects]$ recon-all -make all -s ERROR: Flag -make unrecognized. -make all -s I'm running v3.0.4. Allison Stevens wrote: You can do: "recon-all -make all -s and it will run all the remaining steps that have not been done or are out of date. On Fri, 25 Jan 2008, Chris Watson wrote: Hello, While running recon-all on a subject, my machine logged me off for an unrelated reason. It was stopped during -autorecon3, specifically at -surfreg (mris_register) for the right hemi. The left hemi was already done, I believe. What would be the command to start from that step, and continue to the end? Thanks, Chris ___ 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
Re: [Freesurfer] Aseg.stats file
Jared, You can do recon-all -segstats for each subject. This uses the aseg.mgz to create the aseg.stats, however, if the new aseg.mgz you generated with the script I sent you is named something other than aseg.mgz, then you will want to change it to aseg.mgz for this to work. Allison On Wed, 30 Jan 2008, Jared Conley wrote: FreeSurfer Community, Is there an easy, quick way to regenerate the aseg.stats file? This particular file was deleted accidentally for a few subjects and we wondered if we could quickly recreate this file without having to run recon-all again. All the other files in the subject directory are present. Thanks in advance, Jared ___ 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
Re: [Freesurfer] Assigning Subject Name
Jared, You can do: *recon-all -i **invol1** -i **invol2** -all -subjid **your_subject_name** Allison On Tue, 5 Feb 2008, Jared Morton wrote: When I run the first portion of the recon-all script according to the instructions in RecommendedReconstruction, the command I am instructed to use is: *recon-all -i **invol1** -i **invol2** -autorecon1 -subjid ** your_subject_name* This command allows me to specify the input files and assign them a name. When I try to run the entire recon-all script according to the instructions in FSTutorial/MorphAndRecon, I am instructed to use this command: *recon-all -autorecon-all -s * However, unlike the script for the first portion of the recon-all script, there does not appear to be anything in this command that allows me to specify my input files and assign them a name. Because my subject name is not specified, I cannot get the recon-all script to run. How do I assign a subject name without having to run the first portion of the recon-all script? Any help will be greatly appreciated. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Obtaining cortical parcellations
You can do: recon-all -cortparc -parcstats -s which will create the cortical parcellations and the associated stats file. (Note: -cortparc2 and -parcstats2 will use the alternative atlas). Steps like these can be found on the wiki, here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllStableTablev4 Allison On Wed, 20 Feb 2008, Dan Dillon wrote: Dear FreeSurfers, I have several subjects who have fine inflated, white, and pial surfaces, as well as fine curvatures, but no cortical parcellations. Is there a directive I can pass to recon-all to generate the parcellation without having to run autorecon3 all over again? Something like "-autorecon3-parcellation"? I am running version 4.0.1. Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] change brush configuration defaults in tkmedit
In the meantime, you can make a tcl script with your preferences. Next time you load tkmedit, pass it the tcl flag followed by the path to your tcl script, like this: tkmedit -tcl /path/to/yourscript.tcl The following wiki page shows all the options you can set: https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide_2fTkMeditReference_2fTkMeditScripting It sounds like you're interested in setting these: SetBrushShape SetBrushTarget Allison On Thu, 13 Mar 2008, Bruce Fischl wrote: Hi Ganzalo, we have a new utility that should do this. We'll hopefully have a beta version you can try pretty soon. Check with Ruopeng Wang in a bit. cheers, Bruce On Thu, 13 Mar 2008, Gonzalo Sanchez Benavides wrote: You are right. I'm using the same brush config in several subjects and I want to set this settings by default, if it's possible. Many thanks for your response. 2008/3/12, Bruce Fischl <[EMAIL PROTECTED]>: Thanks Ganzalo, just to be clear- you would like to change the settings and have the new settings load next time you use tkmedit? Bruce On Wed, 12 Mar 2008, Gonzalo Sanchez Benavides wrote: Hi all, Is there the possibility to change the default settings in Tools>Configure Brush Info and Tools>Configure Volume Brush in Tkmedit? How can I change it, please? Many thanks in advance Congratulations to developers for this great software. ___ 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
Re: [Freesurfer] structures list
Lindsay, If you do cd $FREESURFER_HOME You'll find the FreeSurferColorLUT.txt there which has all the labels for cortical and subcortical structures. Allison On Tue, 1 Apr 2008, Lindsay Casmaer wrote: Does the website contain a list of structures labeled in both version 3 and version 4? I am looking for both cortical and subcortical segmentation labels. Thanks, Lindsay ___ 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
Re: [Freesurfer] Bad Talairach
I know someone that uses something like what is below to avoid using tkregister: mri_convert $subject/mri/T1.mgz $subject/mri/T1.mnc mritotal -protocol icbm $subject/mri/T1.mnc $subject/mri/T1.xfm mv $subject/mri/transforms/talairach.xfm $subject/mri/transforms/oldtalairach.xfm cp $subject/mri/T1.xfm $1/mri/transforms/talairach.xfm Doug and Nick can correct me if this isn't a good idea. You can do: mritotal -help to learn more about it. Allison On Sat, 12 Jul 2008, Vina Goghari wrote: Thanks Nick. I was wondering whether since this is a problem for all my subjects (n=70) is there anything else that could fix the problem (i.e. setting some parameter differently etc), so I wouldn't have to do it manually for every subject? Nick Schmansky wrote: Vina, See this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach (you won't need the tutorial data, just use your subject) Nick On Sat, 2008-07-12 at 11:05 -0500, Vina Goghari wrote: Hi all, I get this error: Sat Jul 12 10:24:08 CDT 2008 talairach_avi done # [EMAIL PROTECTED] Talairach Failure Detection Sat Jul 12 10:24:08 CDT 2008 /pkg/bliss_all_labs/tricam/FEP_Aro/cbx02/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0069, pval=0. < threshold=0.0050) Linux bliss 2.6.9-67.0.15.ELsmp #1 SMP Tue Apr 22 13:58:43 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Sat Jul 12 10:24:08 CDT 2008 So I viewed the talairach transform using tkregister2 and this is what I see for target and moveable. How would I go about fixing something like this: See attached images. Thanks, Vina ___ 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
Re: [Freesurfer] Lateral ventricles not filled entirely
You would want to edit the wm.mgz to fill the ventricles in if the surfaces are not accurate. So from your picture, I would say the surfaces do not look accurate in the right hemisphere since they are being pulled into the ventricle. Allison On Tue, 15 Jul 2008, Dorit Kliemann wrote: Hi, I recently started using freesurfer and finally processed my first subjects with all three recon steps (using the latest version). Checking the white matter volume I recognized that all my scans have the same issue: The lateral ventricles aren't filled entirely but there are some black spots within the ventricles..in the tutorial is written that one should handle this in a described way but I was wondering if this is necessary when recon3 was sucessful without any errors. Does anyone have experience with that? (see attached picture) Thanks a lot, Dorit Kliemann ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon with only 1 mprage?
It really shouldn't be a problem to only use one. Using two can give you better SNR but many people have used one successfully - it mostly depends on the quality of your data. For poor quality data, having two might be more necessary. Allison On Mon, 25 Aug 2008 [EMAIL PROTECTED] wrote: Hi! Can anyone tell me what possible issues there are with only using one mprage in creating a recon? [Our first mprage is crashing the reconstruction, and we have found that there was an error of some sort during that mprage, thus the need to do the recon with only the second mprage.] Thanks in advance, Jake ___ 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
Re: [Freesurfer] Surface area measurement
You'll find surface area measurements for each cortical parcellation area in your ?h.aparc.stats file within the stats directory for each subject. Allison On Wed, 3 Sep 2008, Barkay, Gavriel wrote: Can I do surface area measurement using freesurfer? -- Gavriel Barkay M.D. M.Sc. Psychopharmacology Fellow Office: 317-433-1771 Pager: 317-312-2448 ___ 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
Re: [Freesurfer] Bad pial surface - continued
Ed, do you want to send me the subject and I'll take a look?
--
On Mon, 10 May 2010, Ed Gronenschild wrote:
> Hi,
>
> I've mailed this once before and tried to solve a persistent problem.
> Reviewing the results of recon-all I noticed that the derived pial
> surface chopped away an unacceptable amount of gm voxels.
> First of all I tried to manually edit some wm voxels, however with
> no success.
> Then I tried another solution by combining the FSL-FAST wm
> segmentation with wm.mgz because I noticed that FSL_FAST
> produced better results. Although the results did improve,
> still the pial surface was incorrect.
> The last option I tried was another set of parameters for
> nu_correct. Because it concerns 3T scans I used
> --proto-iters1000 and --distance 50 (see paper of Zheng et al,
> NeuroImage 48, 73-83 (2009)) and previous e-mails on
> this subject ("nu-correct parameters", 27 April 2010).
> Also with these settings the pial surface chopped away
> too many voxels.
> I'm desperate, the manuals provide no options on how to fix
> such problems. The pial surface can be corrected by only
> REMOVING voxels that are included erroneously but there is
> no way to extent the pial surface by ADDING voxels.
>
> Ed
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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