Re: [Freesurfer] Subcortical segmentation of a skull-stripped Analyze-formatted image
Can you send us an image? The 16 bit shouldn't be a problem Bruce On Feb 23, 2011, at 7:28 PM, andrewkra...@ucla.edu wrote: > The orig.mgz shows up with weird colors (the grey matter is black, the > background is light gray, and there's a white halo around the brain and in > the ventricles/CSF). > > Another possibility I just thought of is that the original ANALYZE image is > 16-bit, and is 230 x 230 x 230 voxels. Does mri_convert (or any of the > downstream programs) expect the scan to be 8-bit and/or a different size? > > Again, like I said, I'm completely new to Free Surfer (just started trying to > figure it out today), so sorry if this is an obvious first thing to check. > > -- Andrew > > Quoting Bruce Fischl : > >> does the orig.mgz show up properly in tkmedit? >> On Wed, 23 Feb 2011, Nick >> Schmansky wrote: >> >>> add the flag -notal-check to the end of recon-all command to skip the >>> check. >>> >>> if you can make your average using nifti format you're better off as >>> analyze doesnt retain orientation (l/r) info. >>> >>> you may have to manually register the brain following this: >>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach >>> >>> n. >>> >>> >>> On Wed, 2011-02-23 at 13:38 -0800, andrewkra...@ucla.edu wrote: Hello, I'm a complete newbie to FreeSurfer, so I appreciate any and all help you can provide. I am trying to use FreeSurfer to automatically create some masks of subcortical structures, but am having trouble getting the whole process started. When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is my subject name) it quits with the error "ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < threshold=0.0050)" I am trying to do this to a skull-stripped brain originally in Analyze format (there are no DICOMs since it's actually an average of many skull-stripped scans), to which I've already registered all of the scans I want to study. I used mri_convert to convert the .img file into a .mgz file, but compared to the bert example, the background (non-brain area) is a light gray instead of black. I don't know if this is where the error is occuring, and if it is, how to correct it. If it helps, the scan I'm trying to create masks from has been registered to the ICBM brain template. Let me know what other information you need and thanks for the help, -- Andrew ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Converting an ascii file to a freesurfer volume file
If you save it in our ASCII surface format any of our tools should read it, including mris_convert Cheers Bruce On Feb 22, 2011, at 3:35 PM, Tina Jeon wrote: > Hello freesurfers, > > > > I am trying to convert a partially inflated surface .ply file created in afni > to a freesurfer volume so that I can visualize the surfaces via tksurfer. Is > there freesurfer command that converts text to volume, in essence the > converse of mris_convert? And if not can you suggest a way that I can open > the text file using a different graphical interface? > > > > Thank you in advance, > > > > Tina Jeon > > Graduate Student > > Advanced Imaging Research Center > > UT Southwestern Medical Center > > > > > > UT Southwestern Medical Center > The future of medicine, today. > ___ > 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] Subcortical segmentation of a skull-stripped Analyze-formatted image
The orig.mgz shows up with weird colors (the grey matter is black, the background is light gray, and there's a white halo around the brain and in the ventricles/CSF). Another possibility I just thought of is that the original ANALYZE image is 16-bit, and is 230 x 230 x 230 voxels. Does mri_convert (or any of the downstream programs) expect the scan to be 8-bit and/or a different size? Again, like I said, I'm completely new to Free Surfer (just started trying to figure it out today), so sorry if this is an obvious first thing to check. -- Andrew Quoting Bruce Fischl : > does the orig.mgz show up properly in tkmedit? > On Wed, 23 Feb 2011, Nick > Schmansky wrote: > >> add the flag -notal-check to the end of recon-all command to skip the >> check. >> >> if you can make your average using nifti format you're better off as >> analyze doesnt retain orientation (l/r) info. >> >> you may have to manually register the brain following this: >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach >> >> n. >> >> >> On Wed, 2011-02-23 at 13:38 -0800, andrewkra...@ucla.edu wrote: >>> Hello, >>> >>> I'm a complete newbie to FreeSurfer, so I appreciate any and all help >>> you can provide. I am trying to use FreeSurfer to automatically create >>> some masks of subcortical structures, but am having trouble getting >>> the whole process started. >>> >>> When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is >>> my subject name) it quits with the error >>> >>> "ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >>> ***FAILED*** (p=0., pval=0. < threshold=0.0050)" >>> >>> >>> I am trying to do this to a skull-stripped brain originally in Analyze >>> format (there are no DICOMs since it's actually an average of many >>> skull-stripped scans), to which I've already registered all of the >>> scans I want to study. I used mri_convert to convert the .img file >>> into a .mgz file, but compared to the bert example, the background >>> (non-brain area) is a light gray instead of black. I don't know if >>> this is where the error is occuring, and if it is, how to correct it. >>> If it helps, the scan I'm trying to create masks from has been >>> registered to the ICBM brain template. >>> >>> Let me know what other information you need and thanks for the help, >>> -- Andrew >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] {Disarmed} structural sequence for Siemens Verio 3T
Is there a list of recommended MPRAGE parameters for a Siemens Verio 3T machine? The structural protocols on this page: MailScanner has detected a possible fraud attempt from "www.nmrmgh.harvard.edu" claiming to be http://www.nmr.mgh.harvard.edu/~andre/ are for a Sonata (1.5T). I'm not sure what "Gleek 3T" means and again refers to a Sonata. Thanks for your help. Houman ___ 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] Subcortical segmentation of a skull-stripped Analyze-formatted image
does the orig.mgz show up properly in tkmedit? On Wed, 23 Feb 2011, Nick Schmansky wrote: > add the flag -notal-check to the end of recon-all command to skip the > check. > > if you can make your average using nifti format you're better off as > analyze doesnt retain orientation (l/r) info. > > you may have to manually register the brain following this: > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > n. > > > On Wed, 2011-02-23 at 13:38 -0800, andrewkra...@ucla.edu wrote: >> Hello, >> >> I'm a complete newbie to FreeSurfer, so I appreciate any and all help >> you can provide. I am trying to use FreeSurfer to automatically create >> some masks of subcortical structures, but am having trouble getting >> the whole process started. >> >> When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is >> my subject name) it quits with the error >> >> "ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >> ***FAILED*** (p=0., pval=0. < threshold=0.0050)" >> >> >> I am trying to do this to a skull-stripped brain originally in Analyze >> format (there are no DICOMs since it's actually an average of many >> skull-stripped scans), to which I've already registered all of the >> scans I want to study. I used mri_convert to convert the .img file >> into a .mgz file, but compared to the bert example, the background >> (non-brain area) is a light gray instead of black. I don't know if >> this is where the error is occuring, and if it is, how to correct it. >> If it helps, the scan I'm trying to create masks from has been >> registered to the ICBM brain template. >> >> Let me know what other information you need and thanks for the help, >> -- Andrew >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] installation problem
does mri_convert work? glxgears? tksurfer? qdec? freeview? your installation should work on ubuntu, as it has for other people, so i'm a bit at a loss. n. On Thu, 2011-02-24 at 07:12 +0800, Liukarl wrote: > Hello, Nick > > the output of uname -a is > > "Linux Jie-Liu-Linux 2.6.35-25-generic #44-Ubuntu SMP Fri Jan 21 > 17:40:48 UTC 2011 i686 GNU/Linux" > > thanks > > Jie > > > > > > Subject: Re: [Freesurfer] installation problem > > From: ni...@nmr.mgh.harvard.edu > > To: remembe...@hotmail.com > > CC: freesurfer@nmr.mgh.harvard.edu > > Date: Wed, 23 Feb 2011 11:59:16 -0500 > > > > what is the output of > > > > uname -a > > > > > > On Thu, 2011-02-24 at 00:53 +0800, Liukarl wrote: > > > Hello, Freesurfer experts: > > > > > > > > > > > > I emailed some installation problems a couple days ago, but > haven’t > > > answered yet. I am new to freesurfer and try to install the newest > > > version of freesurfer in Ubuntu system. I closely followed the > > > instructions, and the only difference is that I installed it in my > > > Documents, instead of local folder. > > > > > > > > > > > > > > > > > > Below is the output after “source > $FREESURFER_HOME/SetUpFreeSurfer.sh” > > > > > > > > > > > > > > > > > > freesurfer-Linux-centos4-stable-pub-v5.0.0 > > > > > > > > > > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > > > > > > > > > > > FREESURFER_HOME /home/jie/Documents/freesurfer/ > > > > > > > > > > > > FSFAST_HOME /home/jie/Documents/freesurfer//fsfast > > > > > > > > > > > > FSF_OUTPUT_FORMAT nii > > > > > > > > > > > > SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects > > > > > > > > > > > > MNI_DIR /home/jie/Documents/freesurfer//mni > > > > > > > > > > > > Everything seems fine and I also added the .license file to the< > br>> > freesurfer folder. But when I test it by “tkmedit bert > orig.mgz”, it > > > reponds “Illegal instruction” > > > > > > > > > > > > If I type in “recon-all”, it will show > > > > > > > > > > > > “ Required Arguments: > > > > > > > > > > > > -subjid > > > > > > > > > > > > -…... ” and the other arguments. > > > > > > > > > > > > > > > > > > How to fix the problem and make Fressurfer run? Any help is > > > appreciated. Thanks a lot! > > > > > > > > > > > > > > > > > > PS: my Ubuntu is 32-bit and choose the 32-bit version Freesurfer. > > > > > > > > > > > > Jie > > > > > > ___ > > > 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] installation problem
Hello, Nick the output of uname -a is "Linux Jie-Liu-Linux 2.6.35-25-generic #44-Ubuntu SMP Fri Jan 21 17:40:48 UTC 2011 i686 GNU/Linux" thanks Jie > Subject: Re: [Freesurfer] installation problem > From: ni...@nmr.mgh.harvard.edu > To: remembe...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Date: Wed, 23 Feb 2011 11:59:16 -0500 > > what is the output of > > uname -a > > > On Thu, 2011-02-24 at 00:53 +0800, Liukarl wrote: > > Hello, Freesurfer experts: > > > > > > > > I emailed some installation problems a couple days ago, but haven’t > > answered yet. I am new to freesurfer and try to install the newest > > version of freesurfer in Ubuntu system. I closely followed the > > instructions, and the only difference is that I installed it in my > > Documents, instead of local folder. > > > > > > > > > > > > Below is the output after “source $FREESURFER_HOME/SetUpFreeSurfer.sh” > > > > > > > > > > > > freesurfer-Linux-centos4-stable-pub-v5.0.0 > > > > > > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > > > > > > > FREESURFER_HOME /home/jie/Documents/freesurfer/ > > > > > > > > FSFAST_HOME /home/jie/Documents/freesurfer//fsfast > > > > > > > > FSF_OUTPUT_FORMAT nii > > > > > > > > SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects > > > > > > > > MNI_DIR /home/jie/Documents/freesurfer//mni > > > > > > > > Everything seems fine and I also added the .license file to the > > freesurfer folder. But when I test it by “tkmedit bert orig.mgz”, it > > reponds “Illegal instruction” > > > > > > > > If I type in “recon-all”, it will show > > > > > > > > “ Required Arguments: > > > > > > > > -subjid > > > > > > > > -…... ” and the other arguments. > > > > > > > > > > > > How to fix the problem and make Fressurfer run? Any help is > > appreciated. Thanks a lot! > > > > > > > > > > > > PS: my Ubuntu is 32-bit and choose the 32-bit version Freesurfer. > > > > > > > > Jie > > > > ___ > > 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] Subcortical segmentation of a skull-stripped Analyze-formatted image
mri_convert --help has info on specifying orientation, with suitable warnings about the need for you to make sure you know which way is correct. n. On Wed, 2011-02-23 at 14:55 -0800, andrewkra...@ucla.edu wrote: > Thanks for the reply. For the orientation, I know from working with > the sources of the average that it's in neurological (left = left) > orientation. Is there a way to let mri_convert know this (it looks > like ANALYZE is usually radiological so I don't know if this is what > is assumed)? Unfortunately I don't know if it's possible to make the > average in nifti format instead, since everything is currently set up > using ANALYZE (i.e. the scans it's averaging are already in ANALYZE). > > -- Andrew > > Quoting Nick Schmansky : > > > add the flag -notal-check to the end of recon-all command to skip the > > check. > > > > if you can make your average using nifti format you're better off as > > analyze doesnt retain orientation (l/r) info. > > > > you may have to manually register the brain following this: > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > > > n. > > > > > > On Wed, 2011-02-23 at 13:38 -0800, andrewkra...@ucla.edu wrote: > >> Hello, > >> > >> I'm a complete newbie to FreeSurfer, so I appreciate any and all help > >> you can provide. I am trying to use FreeSurfer to automatically create > >> some masks of subcortical structures, but am having trouble getting > >> the whole process started. > >> > >> When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is > >> my subject name) it quits with the error > >> > >> "ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > >> ***FAILED*** (p=0., pval=0. < threshold=0.0050)" > >> > >> > >> I am trying to do this to a skull-stripped brain originally in Analyze > >> format (there are no DICOMs since it's actually an average of many > >> skull-stripped scans), to which I've already registered all of the > >> scans I want to study. I used mri_convert to convert the .img file > >> into a .mgz file, but compared to the bert example, the background > >> (non-brain area) is a light gray instead of black. I don't know if > >> this is where the error is occuring, and if it is, how to correct it. > >> If it helps, the scan I'm trying to create masks from has been > >> registered to the ICBM brain template. > >> > >> Let me know what other information you need and thanks for the help, > >> -- Andrew > >> ___ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to whom it is > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > contains patient information, please contact the Partners Compliance > > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to > > you in error > > but does not contain patient information, please contact the sender > > and properly > > dispose of the e-mail. > > > > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Subcortical segmentation of a skull-stripped Analyze-formatted image
add the flag -notal-check to the end of recon-all command to skip the check. if you can make your average using nifti format you're better off as analyze doesnt retain orientation (l/r) info. you may have to manually register the brain following this: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach n. On Wed, 2011-02-23 at 13:38 -0800, andrewkra...@ucla.edu wrote: > Hello, > > I'm a complete newbie to FreeSurfer, so I appreciate any and all help > you can provide. I am trying to use FreeSurfer to automatically create > some masks of subcortical structures, but am having trouble getting > the whole process started. > > When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is > my subject name) it quits with the error > > "ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > ***FAILED*** (p=0., pval=0. < threshold=0.0050)" > > > I am trying to do this to a skull-stripped brain originally in Analyze > format (there are no DICOMs since it's actually an average of many > skull-stripped scans), to which I've already registered all of the > scans I want to study. I used mri_convert to convert the .img file > into a .mgz file, but compared to the bert example, the background > (non-brain area) is a light gray instead of black. I don't know if > this is where the error is occuring, and if it is, how to correct it. > If it helps, the scan I'm trying to create masks from has been > registered to the ICBM brain template. > > Let me know what other information you need and thanks for the help, > -- Andrew > ___ > 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] Subcortical segmentation of a skull-stripped Analyze-formatted image
Hello, I'm a complete newbie to FreeSurfer, so I appreciate any and all help you can provide. I am trying to use FreeSurfer to automatically create some masks of subcortical structures, but am having trouble getting the whole process started. When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is my subject name) it quits with the error "ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < threshold=0.0050)" I am trying to do this to a skull-stripped brain originally in Analyze format (there are no DICOMs since it's actually an average of many skull-stripped scans), to which I've already registered all of the scans I want to study. I used mri_convert to convert the .img file into a .mgz file, but compared to the bert example, the background (non-brain area) is a light gray instead of black. I don't know if this is where the error is occuring, and if it is, how to correct it. If it helps, the scan I'm trying to create masks from has been registered to the ICBM brain template. Let me know what other information you need and thanks for the help, -- Andrew ___ 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] mri_surfcluster -ocn
Hi all, We ran mri_surfcluster on our group data (we didn't do montecarlo simulations), so we used our .mgh file. We used the -ocn flag to make an output file so we could look at the specific clusters. When we looked at the data of the ocn file using tksurfer, the most significant cluster wasn't visible at the .05 level (which is the min threshold we specified in the mri_surfcluster). We tried playing with the threshold, but it was the opposite of what we expected. The most significant clusters disappeared at the lowest threshold but the less significant ones appeared even when we raised the threshold. This happened when we ran the other hemisphere as well. Do you have any idea how to fix this? we are using freesurfer v5 subjects_dir: cluster/manoach/milton/subjects Our commands: mri_surfcluster --in ./group_analysis/mct_lh/osgm/sig.mgh --hemi lh --thmin 1.3 --thmax infinity --subject fsaverage --sum ./group_analysis/mct_lh/osgm/mst_v_mct.txt --ocn /cluster/manoach/milton/subjects/group_analysis/mct_lh/osgm/sig.cluster.p05.ocn.mgh tksurfer fsaverage lh inflated -overlay sig.cluster.p05.ocn.mgh Thanks in advance! Best, Mandy Nagy ___ 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] FuncROI in Stable 5
Hi Freesurfers, When conducting ROI analyses in Stable 5, is there a way to generate a mean functional baseline offset value within the ROI which can be used to help calculate percent signal change? This would correspond to the value from row 4 in the output file generated by roisummary-sess in Stable 4. Thanks, Adam PS: Here are examples of the commands I've used in Stable 5 to generate ROI Data: funcroi-config -analysis SIRP_Stable5 -label LH_16MTH_7v1_DLPFC -roi MTH_7vFix_DLPFC.roicfg -contrast Cond7vFix -sign abs -thresh 1.3 funcroi-sess -roi MTH_7vFix_DLPFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/16_PreScan_Genotyped_MTH funcroi-table-sess -roi MTH_7vFix_DLPFC.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/16_PreScan_Genotyped_MTH -c Cond7vFix -o /cluster/roffman/users/Stable5_PerRun/DLPFC_ROI_7vFix_MTH > You need to specify a threshold (-thresh) with a contrast. This is the > equivalent to the -min in funcroi-sess. There was a bug in > funcroi-config that prevented it from catching that you did not specify > a threshold (which has been fixed now). > thanks > doug > > Adam Nitenson wrote: >> Hi Freesurfers, >> >> I'm trying to analyze functional data in Stable 5, but have noticed >> that the func2roi command is no longer used. My analysis involves 9 >> conditions (not including Fixation) and 1 timepoint for each. The >> steps I used in Stable 4 to generate this data are as follows: >> >> func2roi-sess -roidef LH_16MTH_7v1_DLPFC -analysis fmcsm5_functionals >> -anatlabel LH_16MTH_7v1_DLPFC -sf >> /cluster/roffman/users/MTH_Study/Subject_Lists_MTH/16_PreScan_Genotyped >> -d >> /cluster/roffman/users/MTH_Study >> >> roisummary-sess -roidef LH_16MTH_7v1_DLPFC -analysis fmcsm5_functionals >> -sf >> /cluster/roffman/users/MTH_Study/Subject_Lists_MTH/16_PreScan_Genotyped >> -d >> /cluster/roffman/users/MTH_Study -sumfile >> /cluster/roffman/users/MTH_Study/ROI_Analysis/LH_16MTH_7v1Label_DLPFC >> >> In Stable 5, I see that there are several commands, funcroi-config, >> funcroi-sess, and funcroi-table-sess. Looking at other threads, it seems >> like I need to make a roicfg file for each contrast. So far I have >> tried: >> >> funcroi-config -analysis SIRP_Stable5 -label LH_16MTH_7v1_DLPFC -roi >> MTH_7vFix_DLPFC.roicfg -contrast Cond7vFix -sign abs >> >> and then >> >> funcroi-sess -roi MTH_7vFix_DLPFC.roicfg -sf >> /cluster/roffman/users/Stable5_PerRun/Subject_Files/16_PreScan_Genotyped_MTH >> >> ...but for the latter, I get the following error: >> PVF (null) >> Thesholding hit volume. >> done >> mri_binarize --i >> /autofs/cluster/roffman/users/Stable5_PerRun/MTH20002AA/bold/SIRP_Stable5/Cond7vFix/sig.nii >> --frame 0 --mask >> /autofs/cluster/roffman/users/Stable5_PerRun/MTH20002AA/bold/SIRP_Stable5/MTH_7vFix_DLPFC.nii >> --o >> /autofs/cluster/roffman/users/Stable5_PerRun/MTH20002AA/bold/SIRP_Stable5/MTH_7vFix_DLPFC.nii >> --abs --min >> ERROR: --min flag needs 1 argument >> >> I don't see the --min argument described for either funcroi-config or >> funcroi-sess, so I was wondering what I needed to add/change to generate >> data similar to what I did for Stable 4. >> >> >> Thanks, >> >> Adam Nitenson, B.S. >> Brain Genomics Lab >> Massachusetts General Hospital >> niten...@nmr.mgh.harvard.edu >> Phone: 617-643-3215 >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital niten...@nmr.mgh.harvard.edu Phone: 617-643-3215 ___ 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 orientation/registration in the motion correction step
Hi again. The orientation looks correct for both volumes (001.mgz and 002.mgz). Does anyone know what is then going wrong with the registration in Freesurfer? The average volume (orig.mgz) can be seen here: http://freesurfer.nikolasborrel.com/bad_registration.tif Kind regards Nikolas Borrel-Jensen > > ___ 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] installation problem in ubuntu
Dear Pedro, I would like to start with the tutorials but I don't have permission to copy the data to the subjects directory, how I can change this? Best regards, Carolina 2011/2/22 Pedro Paulo de Magalhães Oliveira Junior > try the command: > > sudo apt-get install tcl > > -- PPJ > > Please: cc the freesurfer list when answering > > 2011/2/22 Carolina Valencia > > Hi Pedro, >> >> Finally, I could install it with the license file and the environment is >> properly set without warnings. >> But trying to test it, following the instruction on the wiki page I have a >> problem >> >> cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit bert orig.mgz >> /usr/local/freesurfer/bin/tcl_setup: No existe el fichero o el directorio. >> >> in the .bashrc I copy the right location of the freesurfer folder >> FREESURFER_HOME=/home/cvalencia/freesurfer >> source $FREESURFER_HOME/SetUpFreeSurfer.sh >> >> >> 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior >> >>> run this command >>> >>> sudo rm -rf $FREESURFER_HOME >>> >>> >>> >>> 2011/2/21 Carolina Valencia >>> Thanks Pedro, How I uninstall that version to re-install the correct version? I look for some answers and try rm -rf $FREESURFER_HOME It says that I don't have permission,how I can unistall it, if i'm the admin user? Thanks in advance, Carolina 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior < p...@netfilter.com.br> > It seems you are running the 64-bit version of FreeSurfer in a 32-bit > OS > > > 2011/2/21 Carolina Valencia > > >> Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae >> #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux >> >> Thanks, >> >> >> 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior < >> p...@netfilter.com.br> >> >> Please send the result of the command: >>> >>> uname -a >>> >>> >>> On Mon, Feb 21, 2011 at 10:31, Carolina Valencia < >>> cvalen...@linkdx.com.co> wrote: >>> Hi Bruce, I'm experimenting problems with the installation on Ubuntu too. There's is warning in the welcome message, it seems that something is missing: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist FREESURFER_HOME /home/cvalencia/Descargas/freesurfer FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects MNI_DIR /home/cvalencia/Descargas/freesurfer/mni FSL_DIR /usr/share/fsl/4.1 I try to test it and it shows cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit /home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de ejecutable incorrecto. Binary file not executable. Thanks a lot, Carolina 2011/2/18 Bruce Fischl > Hi Jie, > > what hardware are you using? Is it a 64 bit operating system? > > cheers > Bruce > > On Sat, 19 Feb 2011, Liukarl wrote: > > >> >> >> >> >> >> >> >> >> Hello, Freesurfer experts: >> >> >> >> I am new to freesurfer and try to >> install the newest version of freesurfer in Ubuntu system. I >> closely >> followed the instructions, and the only difference is that I >> installed it in my Documents, instead of local folder. >> >> >> >> Below is the output after “source >> $FREESURFER_HOME/SetUpFreeSurfer.sh” >> >> >> >> >> freesurfer-Linux-centos4-stable-pub-v5.0.0 >> >> Setting up environment for >> FreeSurfer/FS-FAST (and FSL) >> >> FREESURFER_HOME >> /home/jie/Documents/freesurfer/ >> >> FSFAST_HOME >> /home/jie/Documents/freesurfer//fsfast >> >> FSF_OUTPUT_FORMAT nii >> >> SUBJECTS_DIR >> /home/jie/Documents/freesurfer//subjects >> >> MNI_DIR >> /home/jie/Documents/freesurfer//mni >> >> >> >> >> Everything seems fine and I also added >> the .license file to the freesurfer folder. >> >> >> >> But when I test it by “tkmedit bert >> orig.mgz”, it reponds “Illegal instruction” >> >> >> >> If I type in “recon-all”, it will >> show >> >> “
[Freesurfer] ASL tag-control order
Hi, How can I tell what the tag-control order of collection was for my ASL images? They were all acquired in Bay 3. I can get you other parameters if you need... ___ 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] installation problem
what is the output of uname -a On Thu, 2011-02-24 at 00:53 +0800, Liukarl wrote: > Hello, Freesurfer experts: > > > > I emailed some installation problems a couple days ago, but haven’t > answered yet. I am new to freesurfer and try to install the newest > version of freesurfer in Ubuntu system. I closely followed the > instructions, and the only difference is that I installed it in my > Documents, instead of local folder. > > > > > > Below is the output after “source $FREESURFER_HOME/SetUpFreeSurfer.sh” > > > > > > freesurfer-Linux-centos4-stable-pub-v5.0.0 > > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > > > FREESURFER_HOME /home/jie/Documents/freesurfer/ > > > > FSFAST_HOME /home/jie/Documents/freesurfer//fsfast > > > > FSF_OUTPUT_FORMAT nii > > > > SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects > > > > MNI_DIR /home/jie/Documents/freesurfer//mni > > > > Everything seems fine and I also added the .license file to the > freesurfer folder. But when I test it by “tkmedit bert orig.mgz”, it > reponds “Illegal instruction” > > > > If I type in “recon-all”, it will show > > > > “ Required Arguments: > > > > -subjid > > > > -…... ” and the other arguments. > > > > > > How to fix the problem and make Fressurfer run? Any help is > appreciated. Thanks a lot! > > > > > > PS: my Ubuntu is 32-bit and choose the 32-bit version Freesurfer. > > > > Jie > > ___ > 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] installation problem
Hello, Freesurfer experts: I emailed some installation problems a couple days ago, but haven’t answered yet. I am new to freesurfer and try to install the newest version of freesurfer in Ubuntu system. I closely followed the instructions, and the only difference is that I installed it in my Documents, instead of local folder. Below is the output after “source $FREESURFER_HOME/SetUpFreeSurfer.sh” freesurfer-Linux-centos4-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/jie/Documents/freesurfer/ FSFAST_HOME /home/jie/Documents/freesurfer//fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects MNI_DIR /home/jie/Documents/freesurfer//mni Everything seems fine and I also added the .license file to the freesurfer folder. But when I test it by “tkmedit bert orig.mgz”, it reponds “Illegal instruction” If I type in “recon-all”, it will show “ Required Arguments: -subjid -…... ” and the other arguments. How to fix the problem and make Fressurfer run? Any help is appreciated. Thanks a lot! PS: my Ubuntu is 32-bit and choose the 32-bit version Freesurfer. Jie ___ 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] question about qdec analysis
the procedure you followed is correct, although in general you dont need to run make_average_subject, as the default target subject 'fsaverage' is fine for most studies. add -target after -qcache if you did create your own target. per your questions, 2.2, assuming you imported the group subject stats into your qdec.table.dat, those thickness are the raw average thicknesses of a region, prior to an analysis. the thicknesses you see in the Display pertain to the analysis conducted during qdec per your factor selection. 2.3 the qdec.table.dat stores the data pertaining to a group of subjects and only enters into an analysis when particular factors (continuous or discrete vars) are selected, so the number of vars stored in qdec.table.dat does not affect the analysis, only their availability for selection as a factor to conduct an analysis. 3. the wiki examples pertain to an analysis of the 40 subjects found in the tutorial data. your data appears to be different. see also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial n. On Wed, 2011-02-23 at 10:12 +0800, 汪贵宏 wrote: > Hi everybody, > > I am new user of Freesurfer,I simply take five procedures to > process my data ,after I read the wiki on the website. The five > procedures including: > > 1. mri_convert one-dicom-file-from-series blobby.nii.gz > > 2.recon-all -i blobby.nii.gz -subjid blobby –all > > 3.recon-all -s -qcache > > 4.make_average_subject. > > 5.qdec > > Now, my questions are: > > 1.In our e-mail ,you often talk about recon-all, why did I never > across question about it ? > > 2. I tried to run the qdec-tool, but experienced some problems . I got > different thickness in one area. > In detail: > 1. When I open the qdec.table.dat ,the thickness is different > from the thickness got from the display in Find Clusters and Goto Max, > I really do not know why? > 2. Did I get the same results from two different qdec.table.dat , > one qdec.table.dat has 34 Continuous Variables but the other had only > one Continuous Variable ? > > 3.Why did the display from qdec smaller than the examples in the > wiki on the website? > > Such as the pictures follow. > > > > I guess part of my problem is that I'm having trouble understanding > exactly how to use the freesurfer. Can you try to give me a sort of > layman's explanation? > > Thanks for your answer! > > wang > > > > > > ___ > 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] TKSurfer question
Hi Brian can you explain more what you mean? We distribute an average subject (fsaverage) that you could probably use. cheers Bruce On Wed, 23 Feb 2011, Weisinger, Brian (NIH/NIMH) [F] wrote: > Is there a way to get a general generic TK_Surfer output without using a > subject? > > Thanks, > Brian Weisinger > > ___ > 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] fixing hippocampus segmentation
hmm, that is large, but the tiny one-voxel border you showed in your image wouldn't come close to explaining that. Do you want to upload the subject and we'll take a look? Bruce On Wed, 23 Feb 2011, Tetiana Dadakova wrote: > Dear Bruce, > > The problem is that the volumes I get for hippocampus are much larger > than they should be (like 5000 mm^3 for healthy female). Same is for > some other structures. > > Best wishes, > Tanja. > > > On Wed, Feb 23, 2011 at 3:08 PM, Bruce Fischl > wrote: >> Hi Tetiana, >> >> I think what you're seeing are just the consequences of a voxel-based >> segmentation. The borders have to be voxelated. Note that much of this will >> be corrected in the volume calculation that performs a partial-volume >> correction. >> >> cheers >> Bruce >> >> On Wed, 23 Feb 2011, Tetiana Dadakova wrote: >> >>> Dear Bruce, dear all, >>> >>> I attach several images to show where I would like to manually >>> interfere into segmentation process. >>> >>> img1: Hippocampus' volume covers part of amygdala and parahippocampal >>> area. The intensity in these non-hippocampal regions are between >>> 75-95. >>> >>> img2: Segmentation of brain stem (problem point are shown by arrows). >>> This problem repeats more or less for every subject. >>> >>> img3: Edges of thalamus are too "pixelated". I mean, shouldn't the >>> line be smoother? Can this cause overestimation of thalamus' volume? >>> >>> Manual correction (drawing) of all the mis-segmented parts would take >>> a lot of time, so I would like to find out other way of controlling >>> the segmentation process. (Something like "putting control points" >>> would be perfect). >>> >>> Thank you, >>> Tanja. >>> >>> >>> On Mon, Feb 21, 2011 at 2:56 PM, Bruce Fischl >>> wrote: Hi Tanja, Can you send us an image? Is parahippocampal white matter significantly darker than 110? Bruce On Feb 21, 2011, at 6:41 AM, Tetiana Dadakova wrote: > Dear Freesurfer users, > > For some of my subjects Freesurfer strongly overestimates hippocampus' > volume. Is there any way to fix the segmentation of hippocampus by > e.g. adding some control points (like for white matter here > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints)? > > Thank you, > Tanja. > ___ > 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] Help ! Error for generating *.mgz files
Hi Tim, the one run is okay, but the failure of the Talairach is probably an indication that the orientation information is incorrect. Because analyze doesn't specify the orientation, the info you get is just a guess. Bring the orig.mgz up in tkmedit and see if the anatomical views are correct (e.g. if when we say the view is coronal it in fact is). Even if you can orient it properly though you will never know left from right, which essentially makes the data useless. sorry Bruce On Wed, 23 Feb 2011, xiaotian yin wrote: Dear Bruce, Thank you so much for taking care of my stupid questions :) I searched online regarding the ANALYZE vs Dicom, and I understand your point now ... The problem is, for this scan, I am afraid the only data format that I can play with is ANALYZE ... (although there might be Dicom format available on later scans) So ... I tried some other tools and got the orientation information out of the ANALYZE data (not sure if it makes sense ...) 0.7000 0 0 0 0 0.7000 0 0 0 0 1.5000 0 0 0 0 1. I save them in a *.mat file, and seems that mri_convert did the job successfully, I got the *.mgz file. Then I setup the necessary directories ( i.e. my_new_subjects_dir/subj001/mri/orig ), put the *.mgz file there, and launched " recon-all -all -s subj001 ". Then I got some warnings and errors (see below), and here comes my new questions, if you do not mind ... ** Question-1 : After launching recon-all, got a warning immediately (see below). Sorry for my stupid questions ... but what is a typical input I should feed to recon-all ? Two scans of the same whole brain? Or one scan for the left hemisphere scan and another one for the right hemisphere? Or something else ? "WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue." ** Question-2 : The program seems running well after the warning, until it terminates a couple of minutes later, throwing out some error like below. I just have no idea what to do now ... Could you please give me some hints? "ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < threshold=0.0050)" The complete output from recon-all is attached, for your information. If you need the data, is there any way I can send it to you without bothering other members in the mailing list? Thank you ! Best Regards Tim On Sun, Feb 20, 2011 at 9:47 AM, Bruce Fischl wrote: Hi Tim, it doesn't help to convert from analyze to something else. Once you have gone through analyze all direction information is lost. Can you get access to the data before it was converted to analyze in whatever format the scanner produced? Bruce On Sun, 20 Feb 2011, xiaotian yin wrote: Dear Bruce, THanks for the quick response! I searched online for Analyze --> Dicom converter ... no luck ... Also tried to read the Analyze file (*.hdr) into Matlab, ending up with the following info : Filename: 'IA_1_orig.hdr' FileModDate: '04--2010 01:08:20' HdrFileSize: 348 ImgFileSize: 8126464 Format: 'Analyze' FormatVersion: '7.5' Width: 256 Height: 256 BitDepth: 8 ColorType: 'grayscale' ByteOrder: 'ieee-le' HdrDataType: 'volume ' DatabaseName: 'IA_1_%%%.pic.' Extents: 16384 SessionError: -28067 Regular: 1 Dimensions: [256 256 124 1 1] VoxelUnits: '' CalibrationUnits: 'Y??·2w?·' ImgDataType: 'DT_UNSIGNED_CHAR' PixelDimensions: [1x5 single] VoxelOffset: 0 CalibrationMax: 255 CalibrationMin: 0 Compressed: -2.7107e-005 Verified: -2.7172e-005 GlobalMax: 255 GlobalMin: 0 Descriptor: [1x80 char] AuxFile: '?J?· ?ù·? ?oü·°???' Orientation: 'Orientation unavailable' Originator: ' ·???' Generated: ' p' Scannumber: '??· ' PatientID: '' ExposureDate: '' ExposureTime: '' Views: 0 VolumesAdded: 0 StartField: -1209816480 FieldSkip: -1208305456 OMax: -1208193036 OMin: -1208460092 SMax: -1208306728 SMin: -1077308224 Did not see any "hist.orient" field or affine transformation field ... Do you have any recommendations ? Best Tim On Sat, Feb 19, 2011 at 9:46 PM, Bruce Fischl wrote: Hi Tim, the .hdr/.img format is called Analyze, and it doesn't come with orientation informaton. This means that it is easy for example to get a left/right swap that you will never know was in your data. Can you get it in any other format, like dicom, or whatever format it came off the scanner in? If not, you can send us one of the pairs of
Re: [Freesurfer] Neuroimaging Data Processing Workshop 23-24 March 2011, Edinburgh, UK
Registration is now open. https://www.epay.ed.ac.uk/browse/extra_info.asp?compid=1&catid=42&modid=2&prodid=453&deptid=24&prodvarid=0 Best regards, Chris Gorgolewski On 18 February 2011 17:58, Chris Filo Gorgolewski wrote: > Dear all, > > I am delighted to invite you to a Neuroimaging Data Processing > Workshop which will be held on 23-24th of March 2011 at University of > Edinburgh, UK. During the workshop we will cover neuroimaging data > analysis and management with reusable, scalable and reproducible > processing workflows that combine different software packages (such as > SPM, FSL, and FreeSurfer) using NiPyPE framework. The workshop will > also feature talks and demos covering data management, encapsulation > and visualization using PyXNAT and the Connectome Library and Viewer. > More details can be found at the workshop website: > http://nipype.blogspot.com > > Best regards, > Chris Gorgolewski > ___ 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] longitudinal analysis
Hi Nadia, the processing steps look OK. You have several options to analyze the longitudinal data. We do not have a single tool to do everything automatically but there are many tools in FreeSurfer that can do the individual steps depending on what you want to do (as there are many different statistical analyses that people might want to do). If you are interested in comparing e.g. the thickness: the thickness files are in register across time within subject (in the tp.long.base/surf directories). For 2 time points, you could compute the difference (mris_calc ) or percent change and divide by the distance in time (if it is different across subjects). For your case (>2 time points) one option is to compute a single statistic per subject in a first step (e.g. fit a slope through the 7 time points) and then compare the slopes across groups etc. (basically run a glm for each subject and then use mris_prepoc to register the results to some template, stack them and run a final glm to compare groups). A better way to deal with longitudinal data is to use Linear Mixed Models, but for this you are on your own. You could load stuff into matlab and setup your mixed models there or convert the data into tables and load it into some other statistics package. Hope that helps getting you started, best, Martin On Wed, 2011-02-23 at 15:53 +0100, nadia merhoum wrote: > Hello > > I have just started to use FreeSurfer (version 4.5) and have some > questions on the longitudinal stream: > > I have started to process cross-sectionally all time points (7 tp) of > my patients with the following script: > > recon-all–i tpidN.nii –subjid tpidN –all > > Then, created an unbiased template from all time points for each > subject and process it with recon-all with the following script: > > recon-all -base -tp -tp ... -all > > and finally did the longitudinal process to all time points with the > following script: > > recon-all -long -all > > I would like to know if what I have been doing till this final step is > correct or not? > > Iwould like also to know how we could calculate the differences > between tpid1.long.template and tpid2.long.template for example? And > is there any automatic way to do so? > > Thankyou for your help > > Sincerely > > Nadia > > ___ > 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] TKSurfer question
Is there a way to get a general generic TK_Surfer output without using a subject? Thanks, Brian Weisinger ___ 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] longitudinal analysis
Hello I have just started to use FreeSurfer (version 4.5) and have some questions on the longitudinal stream: I have started to process cross-sectionally all time points (7 tp) of my patients with the following script: recon-all –i tpidN.nii –subjid tpidN* –all* Then, created an unbiased template from all time points for each subject and process it with recon-all with the following script: recon-all -base -tp -tp ... -all and finally did the longitudinal process to all time points with the following script: recon-all -long -all I would like to know if what I have been doing till this final step is correct or not? I would like also to know how we could calculate the differences between tpid1.long.template and tpid2.long.template for example? And is there any automatic way to do so? Thank you for your help Sincerely Nadia ___ 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] fixing hippocampus segmentation
Dear Bruce, The problem is that the volumes I get for hippocampus are much larger than they should be (like 5000 mm^3 for healthy female). Same is for some other structures. Best wishes, Tanja. On Wed, Feb 23, 2011 at 3:08 PM, Bruce Fischl wrote: > Hi Tetiana, > > I think what you're seeing are just the consequences of a voxel-based > segmentation. The borders have to be voxelated. Note that much of this will > be corrected in the volume calculation that performs a partial-volume > correction. > > cheers > Bruce > > On Wed, 23 Feb 2011, Tetiana Dadakova wrote: > >> Dear Bruce, dear all, >> >> I attach several images to show where I would like to manually >> interfere into segmentation process. >> >> img1: Hippocampus' volume covers part of amygdala and parahippocampal >> area. The intensity in these non-hippocampal regions are between >> 75-95. >> >> img2: Segmentation of brain stem (problem point are shown by arrows). >> This problem repeats more or less for every subject. >> >> img3: Edges of thalamus are too "pixelated". I mean, shouldn't the >> line be smoother? Can this cause overestimation of thalamus' volume? >> >> Manual correction (drawing) of all the mis-segmented parts would take >> a lot of time, so I would like to find out other way of controlling >> the segmentation process. (Something like "putting control points" >> would be perfect). >> >> Thank you, >> Tanja. >> >> >> On Mon, Feb 21, 2011 at 2:56 PM, Bruce Fischl >> wrote: >>> >>> Hi Tanja, >>> Can you send us an image? Is parahippocampal white matter significantly >>> darker than 110? >>> Bruce >>> >>> >>> >>> On Feb 21, 2011, at 6:41 AM, Tetiana Dadakova >>> wrote: >>> Dear Freesurfer users, For some of my subjects Freesurfer strongly overestimates hippocampus' volume. Is there any way to fix the segmentation of hippocampus by e.g. adding some control points (like for white matter here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints)? Thank you, Tanja. ___ 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] Help ! Error for generating *.mgz files
Dear Bruce, Thank you so much for taking care of my stupid questions :) I searched online regarding the ANALYZE vs Dicom, and I understand your point now ... The problem is, for this scan, I am afraid the only data format that I can play with is ANALYZE ... (although there might be Dicom format available on later scans) So ... I tried some other tools and got the orientation information out of the ANALYZE data (not sure if it makes sense ...) 0.7000 0 0 0 0 0.7000 0 0 0 0 1.5000 0 0 0 0 1. I save them in a *.mat file, and seems that mri_convert did the job successfully, I got the *.mgz file. Then I setup the necessary directories ( i.e. my_new_subjects_dir/subj001/mri/orig ), put the *.mgz file there, and launched " recon-all -all -s subj001 ". Then I got some warnings and errors (see below), and here comes my new questions, if you do not mind ... ** Question-1 : After launching recon-all, got a warning immediately (see below). Sorry for my stupid questions ... but what is a typical input I should feed to recon-all ? Two scans of the same whole brain? Or one scan for the left hemisphere scan and another one for the right hemisphere? Or something else ? "WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue." ** Question-2 : The program seems running well after the warning, until it terminates a couple of minutes later, throwing out some error like below. I just have no idea what to do now ... Could you please give me some hints? "ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < threshold=0.0050)" The complete output from recon-all is attached, for your information. If you need the data, is there any way I can send it to you without bothering other members in the mailing list? Thank you ! Best Regards Tim On Sun, Feb 20, 2011 at 9:47 AM, Bruce Fischl wrote: > Hi Tim, > > it doesn't help to convert from analyze to something else. Once you have > gone through analyze all direction information is lost. Can you get access > to the data before it was converted to analyze in whatever format the > scanner produced? > Bruce > > On Sun, 20 Feb 2011, xiaotian yin wrote: > >> Dear Bruce, >> >> >> THanks for the quick response! >> >> I searched online for Analyze --> Dicom converter ... no luck ... >> >> Also tried to read the Analyze file (*.hdr) into Matlab, ending up >> with the following info : >> >> Filename: 'IA_1_orig.hdr' >> FileModDate: '04--2010 01:08:20' >> HdrFileSize: 348 >> ImgFileSize: 8126464 >> Format: 'Analyze' >> FormatVersion: '7.5' >> Width: 256 >> Height: 256 >> BitDepth: 8 >> ColorType: 'grayscale' >> ByteOrder: 'ieee-le' >> HdrDataType: 'volume ' >> DatabaseName: 'IA_1_%%%.pic.' >> Extents: 16384 >> SessionError: -28067 >> Regular: 1 >> Dimensions: [256 256 124 1 1] >> VoxelUnits: '' >> CalibrationUnits: 'Y??·2w?·' >> ImgDataType: 'DT_UNSIGNED_CHAR' >> PixelDimensions: [1x5 single] >> VoxelOffset: 0 >> CalibrationMax: 255 >> CalibrationMin: 0 >> Compressed: -2.7107e-005 >> Verified: -2.7172e-005 >> GlobalMax: 255 >> GlobalMin: 0 >> Descriptor: [1x80 char] >> AuxFile: '?J?· ?ù·? ?oü·°???' >> Orientation: 'Orientation unavailable' >> Originator: ' ·???' >> Generated: ' p' >> Scannumber: '??· ' >> PatientID: '' >> ExposureDate: '' >> ExposureTime: '' >> Views: 0 >> VolumesAdded: 0 >> StartField: -1209816480 >> FieldSkip: -1208305456 >> OMax: -1208193036 >> OMin: -1208460092 >> SMax: -1208306728 >> SMin: -1077308224 >> >> >> >> Did not see any "hist.orient" field or affine transformation field ... >> >> Do you have any recommendations ? >> >> >> Best >> Tim >> >> >> >> >> On Sat, Feb 19, 2011 at 9:46 PM, Bruce Fischl >> wrote: >>> >>> Hi Tim, >>> >>> the .hdr/.img format is called Analyze, and it doesn't come with >>> orientation informaton. This means that it is easy for example to get a >>> left/right swap that you will never know was in your data. Can you get it >>> in any other format, like dicom, or whatever format it came off the >>> scanner >>> in? >>> >>> If not, you can send us one of the pairs of files that gives the segfault >>> and we'll take a look >>> >>> cheers >>> Bruce >>> >>> >>> >>> On Sat, 19 Feb 2011, xiaotian yin wrote: >>> Hi, Thank you for reading this email ! I am a newbie to Medical Imaging, and am learning to use FreeSurfer for surf
Re: [Freesurfer] fixing hippocampus segmentation
Hi Tetiana, I think what you're seeing are just the consequences of a voxel-based segmentation. The borders have to be voxelated. Note that much of this will be corrected in the volume calculation that performs a partial-volume correction. cheers Bruce On Wed, 23 Feb 2011, Tetiana Dadakova wrote: > Dear Bruce, dear all, > > I attach several images to show where I would like to manually > interfere into segmentation process. > > img1: Hippocampus' volume covers part of amygdala and parahippocampal > area. The intensity in these non-hippocampal regions are between > 75-95. > > img2: Segmentation of brain stem (problem point are shown by arrows). > This problem repeats more or less for every subject. > > img3: Edges of thalamus are too "pixelated". I mean, shouldn't the > line be smoother? Can this cause overestimation of thalamus' volume? > > Manual correction (drawing) of all the mis-segmented parts would take > a lot of time, so I would like to find out other way of controlling > the segmentation process. (Something like "putting control points" > would be perfect). > > Thank you, > Tanja. > > > On Mon, Feb 21, 2011 at 2:56 PM, Bruce Fischl > wrote: >> Hi Tanja, >> Can you send us an image? Is parahippocampal white matter significantly >> darker than 110? >> Bruce >> >> >> >> On Feb 21, 2011, at 6:41 AM, Tetiana Dadakova wrote: >> >>> Dear Freesurfer users, >>> >>> For some of my subjects Freesurfer strongly overestimates hippocampus' >>> volume. Is there any way to fix the segmentation of hippocampus by >>> e.g. adding some control points (like for white matter here >>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints)? >>> >>> Thank you, >>> Tanja. >>> ___ >>> 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] Constrasts in imbalanced design
Hi Freesurfers, I am currently dealing with some examples of group analysis from freesurfer-wikipages (see http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G0V). Could you please give some clarifications in the following scenario: Assume we have four groups MaleRight, MaleLeft, FemaleRight, and FemaleLeft (from factors gender and handedness). Now we want to set a contrast that is equivalent to the question: "Is there a difference between Males and Females regressing out the effects of handedness?" An appropriate contrast would be [0.5 0.5 -0.5 -0.5]. (see http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G0V#Contrast5male-female.mtx) Is that also true for an imbalanced design, where MaleRight and MaleLeft consist of 15 and 5 subjects, respectively? I suspect that in this case the above contrast would weigh MaleLeft more heavily, i.e. each subject in this rather small subgroup would have a greater effect on the final result. If that is true - I am wondering whether the contrast [0.75 0.25 ...] would fix this issue, i.e. adjust for the unbalanced design. Do you have any ideas? Best, Daniel ___ 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.
