Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
Dear Doug, Thank you for your email. You were correct, there are values in the output file from running mri_segstats. I was hoping for your advice on the following: 1) as I used FreeSurferColorLUT.txt and the aparc+aseg.mgz files, are the values extracted from the transformed cbf images the mean value per anatomic region in the same units as the original CBF image? (I am under the impression yes, and so instead of interpreting the sample data listed below as mm3 I would interpret the values as ml / 100 g / min ) 2) While most of the CBF to T1 registrations using the transformation for the PD to the T1 image worked reasonably, there are a few where the registration is a little off (almost exclusively requiring some translation in the SI direction) - what is the best way to correct the registration and generate a better fitting transformation matrix? (either manually or using some other tool) 3) Do I not need to use seg-erode to minimize partial voluming? 4) Is there a way I can use asegstats2table and / or aparcstats2table on the output file I generate from mri_segstats to create a table with values for multiple subjects? (A sample of my current output file from mri_segstats is below). Thank you for all your help. Best wishes, Sal # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ # cmdline mri_segstats --seg aparc+aseg.mgz --ctab /farmshare/software/free/freesurfer/5.3.0/FreeSurferColorLUT.txt --i JK_CBF_Reg.nii.gz --sum JK_ASL.stats --seg-erode 1 # sysname Linux # hostname f.stanford.edu # machine x86_64 # user soman # anatomy_type volume # # SegVolFile aparc+aseg.mgz # SegVolFileTimeStamp 2014/09/21 21:26:30 # ColorTable /farmshare/software/free/freesurfer/5.3.0/FreeSurferColorLUT.txt # ColorTableTimeStamp 2013/05/13 14:21:15 # InVolFile 1534_1_PRE_1200_CBF_Reg.nii.gz # InVolFileTimeStamp 2014/09/21 21:26:30 # InVolFrame 0 # Only reporting non-empty segmentations # VoxelVolume_mm3 1 # TableCol 1 ColHeader Index # TableCol 1 FieldName Index # TableCol 1 Units NA # TableCol 2 ColHeader SegId # TableCol 2 FieldName Segmentation Id # TableCol 2 Units NA # TableCol 3 ColHeader NVoxels # TableCol 3 FieldName Number of Voxels # TableCol 3 Units unitless # TableCol 4 ColHeader Volume_mm3 # TableCol 4 FieldName Volume # TableCol 4 Units mm^3 # TableCol 5 ColHeader StructName # TableCol 5 FieldName Structure Name # TableCol 5 Units NA # TableCol 6 ColHeader Mean # TableCol 6 FieldName Intensity Mean # TableCol 6 Units unknown # TableCol 7 ColHeader StdDev # TableCol 7 FieldName Itensity StdDev # TableCol 7 Units unknown # TableCol 8 ColHeader Min # TableCol 8 FieldName Intensity Min # TableCol 8 Units unknown # TableCol 9 ColHeader Max # TableCol 9 FieldName Intensity Max # TableCol 9 Units unknown # TableCol 10 ColHeader Range # TableCol 10 FieldName Intensity Range # TableCol 10 Units unknown # NRows 112 # NTableCols 10 # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 0 16192691 16192691.0 Unknown5.2913 14.7318 0. 229. 229. 2 2139929 139929.0 Left-Cerebral-White-Matter39.5857 10.3158 0.87.87. 3 4 1447114471.0 Left-Lateral-Ventricle27.8682 9.4901 5.60.55. 4 566 66.0 Left-Inf-Lat-Vent 31.1515 6.315421.48.27. 5 7 9041 9041.0 Left-Cerebellum-White-Matter 44.4476 9.435617.69.52. 6 8 3197931979.0 Left-Cerebellum-Cortex44.5335 8.893014.88.74. 7 10 5372 5372.0 Left-Thalamus-Proper 35.8096 17.488111.95.84. 8 11 1889 1889.0 Left-Caudate 22.4314 7.9514 8.58.50. 9 12 3145 3145.0 Left-Putamen 27.5463 6.785110.57.47. 10 13 954 954.0 Left-Pallidum 25.0922 5.835614.50.36. 11 14 1102 1102.0 3rd-Ventricle 35.0554 12.4595 8.60.52. 12 15 1698 1698.0 4th-Ventricle 38.9694 8.971118.59.41. 13 16 1772117721.0 Brain-Stem37.2733 8.111012.62.50. 14 17 2187 2187.0 Left-Hippocampus 36.8834 10.756913.86.73. 15 18 636 636.0 Left-Amygdala 29.3239 5.479417.42.25. 16 24 387 387.0 CSF 24.8398 9.1261 7.49.42. 17 26 202 202.0 Left-Accumbens-area 44.82
[Freesurfer] Help on DTI pre-processing
Dear all,I have a question regarding the pre-prossesing steps of DTI data.I have 5 different datasets, each with different acquisition parameters, including the number of directions (16, 32 and 64), the b-value (1000, 1300 and 1500) and the magnetic field (1.5 and 3T). Do you think that a single pre-processing procedure can be applied to all of them? or it will vary depending on the acquisition parameters?A second question would be, if the pre-processing steps of FS include some distortion correction using a high-resolution image? If so, could it be replaced by the T2 or a b0?Can you point me to the correct literature of this?Many thanks in advanced for your time and help,Gabriel ___ 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] Converting GIFTI files to Freesurfer files
Hi, I tested this with mris_convert provided by Nick in the link below, and it worked fine. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/ However, mris_convert in dev version gave me the segmentation fault (core dumped). Just FYI! Best, Reza Hi, To convert GIFTI files to the Freesurfer files, I just need to do something like this? mris_convert F99.R.inflated.74k_f99.surf.gii rh.inflated Thanks, Reza ___ 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] Volume to surface coordinates
Hello freesurfers, I would like to identify, in surface/vertex coordinates, certain points in a volume. Is there a straightforward way to obtain relevant transform? Thank you, Marmaduke Woodman ___ 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 and linear mixed effects models
Hi FS, I want to conduct a within-subjects longitudinal analysis, I thought I would be able to run a LME model in QDEC but this doesn't seem to be the case at all, is this correct? It seems I have to do everything using Matlab (big sigh). https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels I have already preprocessed the data: 1) cross for all time points, 2) base, and then 3) long according to the awesome tutorial provided by FS. I have only one group, a patient population that was scanned prior to (bseline) and at various time points (3 time points post) following treatment. Would you agree that the best analytical approach for me would be the LME model, especially since I have a few subjects with a couple of missing post-treatment time points? Is there any way you would recommend another approach using QDEC? Lastly, I have done everything in FS version 5.1, I'm considering upgrading to 5.3, since my freeview software seems to be out of date. It also seems that the Matlab tools I need to run LME are only available in FS version 5.2. At this point a little concerned since I'm hoping I didn't waste a bunch of time just realizing all this now, would upgrading to 5.3 negatively impact all the work I've done thus far using version 5.1? Thanks for the help!! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Pial Surface Incorrect For Native T1
Hi Doug, Thanks for getting back to me and sorry for the delay. Yes I can actually. If I corregister the CT to orig.nii and then pick out the points in freeview they look pretty good. This is a pretty painful process though. Is there an easy way to save a set of points in a text file from freeview? Ideally, I would like to be able to do this with the native pial surface as well, but I still have the problem of it appearing rotated and flipped in freeview. Is there a way to fix this? Thanks again for your help, Best, -Zack On Thu, Sep 18, 2014 at 12:50 PM, Douglas N Greve wrote: > > Can you get it to display correctly on the pial surface in conformed space? > > On 09/17/2014 08:04 PM, Zachary Greenberg wrote: > > Hello Freesurfer experts, > > > > I am having a tough time getting my pial surfaces into the correct > > anatomical space. I work with ECoG Patients, so we have pre-implant > > high resolution T1s (GE SPGR), and post-implant high resolution CTs > > that show the location of ECoG electrodes within the patient's skull. > > Our goal: display ECoG electrodes in their correct positions on the > > patient's native pial surface. > > > > Right now, my pipeline works like this: > > -ACPC align the T1, leave it in LAS orientation. > > -recon-all the acpc T1, using -3T -all -openmp 8 -use-gpu > > -corregister the CT to the acpc T1 (SPM), get electrode coords in T1 > space > > -plot the electrodes on the resultant .pial surface from freesurfer > > > > The problem is, I can definitely tell that the position of the pial > > mesh is off (probably by 10 millimeters or so), as the electrodes > > (which have the correct coordinates from the T1 correg, confirmed > > visually by overlaying the CT on T1) are not in their correct > > positions on the mesh. Likewise, DTI fibers reconstructed from EPIs > > correctly corregistered to the T1 also appear off position within the > > .pial mesh. > > > > Here is what I have tried: > > > > compute the transform from .pial to .pial.native as suggested on > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat > > > > tkregister2 --mov rawavg.mgz --targ orig.mgz --reg register.native.dat > --noedit --regheader > > mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz > --tval lh.pial.native --tval-xyz --hemi lh --s subjectname > > This results in a mesh that is flipped (left is right) and rotated > > such that anterior is inferior (frontal cortex is pointing downward). > > The mesh appears this way when plotted in any viewer besides > > freesurfer (MATLAB mesh, Pyqt) but appears in the correct orientation > > in freeview. Replacing orig.mgz with the original T1.nii in the > > command above produces the opposite effect, freeview plots the > > orientation wrong, and any other viewer plots the Mesh oriented > > correctly, and the mesh appears to be identical to the originally > > output .pial mesh (electrodes are still wrong). > > > > Any help in pin pointing what is going wrong here would be greatly > > appreciated. I have a feeling it has something to do with the mesh > > being in surface RAS and the original T1 being in LAS. > > > > Thanks a bunch, > > -Zack > > > > > > > > > > > > ___ > > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > 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. > > -- *Zachary Greenberg* *Assistant Imaging Specialist* *Department of Neurological Surgery* *University of California, San Francisco* ___ 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 con
[Freesurfer] Segfault Error
Hi, I am currently running Freesurfer on Linux and while trying to test it out on the bert subject I received the error message: ERROR: A segfault has occurred. This is not your fault, but is most likely an unrecoverable error and has made the program unstable. Please send the contents of the file .xdebug_tkmedit that should be in this directory to freesurfer@nmr.mgh.harvard.edu. I searched high and low for the .xdebug_tkmedit file but could not find it, as it seems the system is not even creating this file. Do you have any suggestions on fixing this issue? Sincerely, Nikita Zhitkevich ___ 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] how to extract the individual cortical thickness or volume value of significant cluster after RFT correction
Dear experts I have question regarding extracting the individual cortical volume value of significant cluster after RFT correction. I have 209 subjects in an analysis and G_pariet_inf-Angular showing significant correction with score of autism after RFT correction using command of mri_surfrft_jlbr in Matlab, how do I export individual subjects cortical volume values for significant regions ? In addition, I did not analyze it using QDEC and just use command following reference (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis)Thank you and hope for responses. With best Regards,kangcheng Wang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] how to extract the individual cortical thickness or volume value of significant cluster after RFT correction
Dear experts I am sorry. There was some wrong with previous description. The results showed that G_pariet_inf-Angular was significantly positive correlated with score of autism after RFT correction using command of mri_surfrft_jlbr. With best Regards,kangcheng Wang ___ 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.
