Freesurfer

freesurfer@nmr.mgh.harvard.edu

2 participants
30134 discussions

BVECS and BVALS file
by Alan Francis 18 Feb '14

18 Feb '14

Hi Anastasia: Hope all is well. I have DTI data for 65 brains. They are in nifti format. However, they do not have the bvecs and bvals information. I searched the web but they only have the conversion information for dicom files. I opened the header on MRICRON but how does one convert these values into table form. thanks so much, Alan Martinos Center.

2 4

Which is broken - GCC or Freesurfer build?
by Durai Arasan 18 Feb '14

18 Feb '14

Hi Freesurfer experts, so I got this error when I ran recon-all on my cluster. I am really hoping this is just a case of missing GCC libraries and nothing is wrong with the Freesurfer installation on the nodes. Kindly confirm this. Thank you ********************************************************************************************************************************** Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /****************** Actual FREESURFER_HOME /************************************** Linux ***************************** SMP Fri Mar 22 05:41:51 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_convert) mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_convert) mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_convert) tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by tkregister2_cmdl) tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by tkregister2_cmdl) tkregister2_cmdl: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by tkregister2_cmdl) mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_make_uchar) mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_make_uchar) mri_make_uchar: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_make_uchar) mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_normalize) mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_normalize) mri_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_normalize) mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_watershed) mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_watershed) mri_watershed: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_watershed) mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_gcut) mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_gcut) mri_gcut: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_gcut) mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_segment) mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_segment) mri_segment: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_segment) mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_label2label) mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_label2label) mri_label2label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_label2label) mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_em_register) mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_em_register) mri_em_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_em_register) mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_ca_normalize) mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_ca_normalize) mri_ca_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_ca_normalize) mri_ca_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_ca_register) mri_ca_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_ca_register) mri_ca_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_ca_register) mri_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_ca_label) mri_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_ca_label) mri_ca_label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_ca_label) mri_pretess: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_pretess) mri_pretess: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_pretess) mri_pretess: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_pretess) mri_fill: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_fill) mri_fill: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_fill) mri_fill: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_fill) mri_tessellate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_tessellate) mri_tessellate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_tessellate) mri_tessellate: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_tessellate) mri_concatenate_lta: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_concatenate_lta) mri_concatenate_lta: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_concatenate_lta) mri_concatenate_lta: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_concatenate_lta) mri_normalize_tp2: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_normalize_tp2) mri_normalize_tp2: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_normalize_tp2) mri_normalize_tp2: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_normalize_tp2) mris_smooth: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_smooth) mris_smooth: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_smooth) mris_smooth: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_smooth) mris_inflate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_inflate) mris_inflate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_inflate) mris_inflate: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_inflate) mris_curvature: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_curvature) mris_curvature: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_curvature) mris_curvature: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_curvature) mris_sphere: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_sphere) mris_sphere: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_sphere) mris_sphere: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_sphere) mris_fix_topology: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_fix_topology) mris_fix_topology: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_fix_topology) mris_fix_topology: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_fix_topology) mris_topo_fixer: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_topo_fixer) mris_topo_fixer: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_topo_fixer) mris_topo_fixer: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_topo_fixer) mris_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_ca_label) mris_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_ca_label) mris_ca_label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_ca_label) mris_euler_number: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_euler_number) mris_euler_number: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_euler_number) mris_euler_number: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_euler_number) mris_make_surfaces: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_make_surfaces) mris_make_surfaces: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_make_surfaces) mris_make_surfaces: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_make_surfaces) mris_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_register) mris_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_register) mris_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_register) mris_volmask: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_volmask) mris_volmask: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_volmask) mris_volmask: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_volmask) mris_anatomical_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_anatomical_stats) mris_anatomical_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_anatomical_stats) mris_anatomical_stats: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_anatomical_stats) mrisp_paint: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mrisp_paint) mrisp_paint: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mrisp_paint) mrisp_paint: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mrisp_paint) mris_curvature_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_curvature_stats) mris_curvature_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_curvature_stats) mris_curvature_stats: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_curvature_stats) mris_calc: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mris_calc) mris_calc: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mris_calc) mris_calc: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mris_calc) mri_robust_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_robust_register) mri_robust_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_robust_register) mri_robust_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_robust_register) mri_robust_template: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_robust_template) mri_robust_template: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_robust_template) mri_robust_template: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_robust_template) mri_and: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_and) mri_and: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_and) mri_and: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_and) mri_or: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_or) mri_or: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_or) mri_or: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_or) mri_fuse_segmentations: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_fuse_segmentations) mri_fuse_segmentations: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_fuse_segmentations) mri_fuse_segmentations: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_fuse_segmentations) mri_segstats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_segstats) mri_segstats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_segstats) mri_segstats: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_segstats) /****************/***444 mri_convert /********************/***_mp.nii /*******************/****444/mri/orig/001.mgz mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_convert) mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_convert) Linux ************************************ ************************ SMP Fri Mar 22 ******** EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ***444 exited with ERRORS at Mon Feb 17 02:24:00 EST 2014 For more details, see the log file **********************/***444/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

3 2

Re: [Freesurfer] [Fwd: Resample a mask on diffusion images using bbregister registration matrix]
by Douglas Greve 18 Feb '14

18 Feb '14

oops, sorry! That command looks like it is correct. Can you say more about what is going wrong? How are you determining that something is going wrong? doug On 2/17/14 9:30 PM, Celine Louapre wrote: > Hi Doug > I don't know if you had the chance to read my email below to resample a > lesion mask on diffusion images. Anastasia gave me the registration file > to use (anatorig2diff.bbr.dat) in the command but the output mask file was > not registered anymore. So she asked me to rephrase my question more > generally on the mailing list to look for help with bbregister. > Thanks a lot > Celine > > > ---------------------------- Original Message ---------------------------- > Subject: [Freesurfer] Resample a mask on diffusion images using bbregister > registration matrix > From: "Celine Louapre" <celine(a)nmr.mgh.harvard.edu> > Date: Thu, February 13, 2014 9:58 pm > To: freesurfer(a)nmr.mgh.harvard.edu > -------------------------------------------------------------------------- > > Hello freesurfer team > I have binary lesions mask from T2star images (resolution 0.3*0.3*1) > already registered on freesurfer space that I would like to resample on > diffusion images to further exclude the lesion voxels on the DTI maps (and > to calculate DTI metrics within the lesions too). > Using mri_vol2vol command I think I am missing something because I tried > with the registration file produced by bbregister (through tracula) but > the result does not look correct. > I have the lesion mask in the freesurfer space that I can overlay on > brainmask or dtifit_FA.nii on freeview and it seems correctly registered > on both. > The command I am running is: > mri_vol2vol --mov recons_dir/subj1/dmri/lowb.nii.gz --targ > /lesion_mask/subj1/lesion_WM.nii.gz --interp nearest --o > /lesion_mask/subj1/lesion_WM_vol2vol.nii.gz --reg > recons_dir/subj1/dmri/xfms/anatorig2diff.bbr.dat --no-save-reg --inv > > And then when I open lesion_WM_vol2vol.nii.gz in freeview, the voxel size > is the same as the DTI images, but the lesions are not at the same place. > > On the mailing list I have also seen other options but I am not sure if > they would be appropriate? > I have seen mri_label2vol command where I could set the fill threshold > parameter but it does not solve the problem of the registration file? > also mri_convert > And eventually I also saw this command: > mri_mask but I guess that the mask volume needs to be in the same > dimension as the diffusion space? > > Thanks a lot > Best > Celine > > >

2 5

postdoc in brain image analysis
by Thomas Yeo 18 Feb '14

18 Feb '14

Dear All, I am looking for a postdoc to work on brain image analysis, e.g., dynamic functional connectivity. See more information below. Regards, Thomas Job Title: Postdoctoral Fellow in Brain Image Analysis Project: Develop novel image analysis and machine learning tools for brain image analysis, (e.g. Dynamic Functional Connectivity). Research Webpage: http://yeolab.weebly.com/research.html Requirements: Ph.D. in computer science, electrical engineering, statistics or related fields. Candidates should have previously published research in image processing, computer vision, statistical or machine learning. Experience with functional MRI is preferred (but not required). Compensation: Competitive and commensurate with experience Institutes: Perform ground-breaking research at the National University of Singapore (NUS), while enjoying the beautiful sceneries and cultures of South-East Asia. NUS is a research-intensive university consistently ranked among the top 30 universities in the world (http://en.wikipedia.org/wiki/National_University_of_Singapore#University_ra…) Successful candidates may be required to travel between Singapore and Harvard Medical School for certain projects. Contact: Email BT Thomas Yeo (thomas.yeo(a)nus.edu.sg) with your CV. Deadline: 1st May, 2014

1 0

trac-all -qa
by Gerit Pfuhl 17 Feb '14

17 Feb '14

Dear Freesurfer experts, we are curious whether we can run trac-all -qa in 5.3. and use it as regressors with our results from tracula 5.2. I.e. is it advisable or shall we run the complete analysis? Thanks, Gerit Pfuhl

2 1

Exporting mask file into Brainvoyager
by Dave Frank 17 Feb '14

17 Feb '14

Hello, I'm trying to use anatomical regions of a subject labeled by freesurfer as an fMRI mask in brainvoyager. I'm using mri_convert to change aparc+aseg.mgz to a nifti, and then changing that into a brainvoyager vmr file. However, the vmr file in brainvoyager looks wrong (see attached screenshot). My conversion command is "mri_convert --in_type mgz --out_type nii --input_volume aparc+aseg.mgz --output_volume aparc+aseg.nii". Has anyone successfully imported freesurfer segmentation volumes to use as masks in branvoyager? Any advice would be greatly appreciated. Thanks! -Dave [image: Inline image 1]

2 2

tkmedit and masking
by Joerg Pfannmoeller 17 Feb '14

17 Feb '14

Hello, I am using tkmedit to display functional data as an overlay on anatomical data. I am asking myself if there is a feature in tkmedit which allows to apply a mask to the functional. Ideally would be a cortex mask to remove all non-cortex voxels. Regards Joerg -- Joerg Pfannmoeller <pfannmoelj(a)uni-greifswald.de>

2 1

large topological defect
by Gregory Kirk 17 Feb '14

17 Feb '14

im trying something novel with a veryb young brain, i ran freesurfer standard stream and got decent results and then did some manual editing to fix a skull struip problem and reran and now it is detecting a large defect, is there a way i can look at the data to see what topological defect it is finding and where ? greg

3 2

Re: [Freesurfer] Optseq download
by Douglas Greve 17 Feb '14

17 Feb '14

Hi Goi, please remember to post to the freesurfer list. Thanks! The max psd depends upon how long it takes for the HRF to return to baseline (and do not related to the TR). This is usually something like 20 sec + the duration of your stimulus. doug On 2/17/14 1:31 PM, Goi Khia Eng wrote: > Dear Prof, Previously I was having problems running optseq, and so > have left it off for a while. I have went back to try again, and > managed to get it to churn sequences. Thank you very much for your > advice and patience. > I have one more query: How much do you think we should set the psdmax > if we have TR of 1, and 2? > > Thanks for your advice! > Regards > Goi khia > > > On Tue, Nov 12, 2013 at 11:50 AM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > are you running "optseq" or "optseq2"? It should be optseq2. You > may need to make it executable (looks like you have the right > chmod command line, but don't put the "./" before it). I can't see > what you are trying to accomplish with the find command. Once you > have it exectuable, you should be able to run it with ./optseq2 > (if it is in the current directory). > doug > > > > On 11/10/13 12:06 PM, Goi Khia Eng wrote: >> Dear Doug, >> >> Thanks so much for your reply. I've downloaded VirtualBox, and >> have also loaded Ubuntu linux OS into the VirtualBox. I managed >> to put in the linux version of optseq2, but was unable to get it >> to run or locate the file. I've ran commands via the terminal >> using terms such as ./optseq2 , ./chmod a+x optseq2, find~/ -type >> f -name "optseq2". However, the messages that I get are either >> "optseq: command not found" or "No such file or directory.". I >> suspect this could be due to my limited knowledge on using linux OS. >> Do you happen to have a manual that you could share on how to >> load Optseq? >> >> Any advice would be very helpful. >> Thanks much! >> Regards >> Goi khia >> >> >> On Sun, Nov 10, 2013 at 1:41 AM, Douglas Greve >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> >> >> Hi Goi khia, it does not really run under windows. The >> version there is if you have a program called CygWin which is >> a linux emulator. We have not used that in a long time. You >> can do the same thing with VirtualBox (another linux emulator >> that runs under windows). >> doug >> >> >> >> >> >> On 11/9/13 12:17 PM, Goi Khia Eng wrote: >>> Dear Prof Greve, >>> >>> I am trying to download Optseq from >>> http://surfer.nmr.mgh.harvard.edu/optseq/ on my Windows >>> machine (Windows 7), but an error message keeps coming up, >>> that cygwin1.dll is missing. >>> I've downloaded the cygwin file from cygwin.com >>> <http://cygwin.com>, but am still unable to download Optseq, >>> and the same error message appears. >>> >>> Do you have any advice on how I can try to resolve this? >>> Thanks much! >>> >>> Regards >>> Goi khia >> >> 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. >> >> > >

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Fwd: Edit hyperintense regions in aseg.mgz file in long or base?
by Linn Christin Bonaventure Norbom 17 Feb '14

17 Feb '14

---------- Forwarded message ---------- From: Linn Christin Bonaventure Norbom <linnnorbom(a)gmail.com> Date: Mon, Feb 10, 2014 at 4:06 PM Subject: Edit hyperintense regions in aseg.mgz file in long or base? To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Hi everyone, I am registering hyperintense lesions as "lh-lesion" or "rh-lesion" and I was wondering if it is better to do this as the base or the long stage. I see that the freesurfer wiki page says I can do it at both stages depending on the problem, but I was not sure if lesion registration counted as "incorrect labeling" or "correcting the volume of importaint structures". Thank you in advance! Regards Linn Norbom

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