[Freesurfer] Freeview screenshot automation questions
Dear FreeSurfer experts, I understand that freeview -v brain.nii.gz -ss screenshot takes the screenshots and quits the freeview. Regarding this, I have the following two questions. (1) Is it possible to suppress the redundant GUI flashing? It is really a pain when many images are batch-processed, because the GUI keeps flashing up and closing. (2) Is it possible to take multiple screenshots with one session? I wish to screenshot multiple slices of one image. I have tried freeview -v brain.nii.gz\ -viewport sagittal -slice 80 127 127 -ss sag1 \ -viewport sagittal -slice 127 127 127 -ss sag2 \ -viewport sagittal -slice 156 127 127 -ss sag3 \ However, the session ends right after the first -ss, producing only one screenshot (sag1.png). I can surely do freeview -v brain.nii.gz 3 times to get these 3 screenshots, but that is very inefficient. Thank you very much for your help in advance! Best regards, Xiuming ZHANG (Eric) Xiuming ZHANG (Mr.) :: Department of Electrical Computer Engineering (ECE) :: National University of Singapore (NUS)___ 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] exporting QDEC results
Dear FreeSurfers, can anybody tell me if there is a way to export results in form of table (or text file) from the QDEC GUI after having performed analysis on thickness, area, volume, etc etc... ? I mean, is the infomation regarding the significant clusters saved in table format? Thank you. Best, Elisa -- Elisa Veronese - PhD *Research Unit on Brain Imaging and Neuropsychology (RUBIN)* *Inter-University Center for Behavioral Neurosciences (ICBN)University of Udine and University of Verona, ItalyICBN Website: http://icbn.uniud.it/tiki-index.php http://icbn.uniud.it/tiki-index.php* ___ 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] quick quality assessment for MPRAGE images
Dear Freesurfer Users, I have a large number of T1 MPRAGE scans collected on a 3T Siemens Trio scanner that I would like to run through recon-all to get cortical thickness values. However, some of the MPRAGE scans are contaminated by subject motion, but the extent of this varies from scan to scan. Is there a quick automated way to assess whether each MPRAGE is high-quality enough to bother with running through recon-all? Thanks! Ezra *___* *Ezra Wegbreit, PhD* NIMH T32 Post-doctoral Research Fellow in Child Mental Health Pedi-MIND Program at Bradley Hospital Department of Psychiatry and Human Behavior Brown University Medical School (401) 432-1615 ezra_wegbr...@brown.edu (preferred) ewegbr...@lifespan.org *___* ___ 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] DWI questions
Dear Freesurfer and DTI experts,I will start some analyses with DWI data, but I have some doubts about it:1) I have data with 5 different acquisition protocols, so, I'm not sure if the standard pre-processing protocol (like eddy-current compensations the reorientation of the vectors and the intra-subject registration) can be applied to all images equally or if I do need to set any specific parameters for each acquisition protocol?2) Does your method have any tool to check that the vectors are good, before or after fitting the tensors?Many thanks in advanced,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] mri_vol2surf
Hi Nicholas mri_vol2surf has options that lets you control its behavior. It can do various types of sampling (e.g. averaging within the cortical ribbon, point sampling at a specified distance or percentage, etc) cheers Bruce On Thu, 18 Sep 2014, Nicholas Heugel wrote: I looked over the documentation but can;t seem to find what I am looking for. How exactly does the function project the mdi data onto the surface? What method is it using to accomplish this, is it just projecting to the nearest neighbor or is there something more complex occurring. I ask because I just want to make sure I completely understand what every step in my analysis is doing and not have it be a blackbox that I put data in and it gives me stuff out. Thanks for your help. Nicholas ___ 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] problem with mris_preproc
Hi, I get the following error message when running mris_preproc, and I'm wondering what file is it looking for?: Reading curvature file /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) MRISreadCurvature: could not open /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) No such file or directory ERROR: reading curvature file This subject, 007, seems to have all the files it should: [rimol @ ~/subjects/long/long_v0v2_amd]$ ls /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf lh.area lh.inflated.H lh.pial_lgi lh.smoothwm.K1.crv lh.thicknessrh.avg_curv rh.orig rh.smoothwm.BE.crv rh.smoothwm.S.crv rh.white lh.area.mid lh.inflated.K lh.pial-outer-smoothed lh.smoothwm.K2.crv lh.volume rh.curv rh.orig_pialrh.smoothwm.C.crv rh.sphere lh.area.pial lh.jacobian_white lh.smoothwm lh.smoothwm.K.crv lh.w-g.pct.mgh rh.curv.pial rh.orig_white rh.smoothwm.FI.crv rh.sphere.reg lh.avg_curv lh.origlh.smoothwm.BE.crv lh.smoothwm.S.crv lh.whiterh.inflated rh.pial rh.smoothwm.H.crv rh.sulc lh.curv lh.orig_pial lh.smoothwm.C.crv lh.sphere rh.area rh.inflated.H rh.pial_lgi rh.smoothwm.K1.crv rh.thickness lh.curv.pial lh.orig_white lh.smoothwm.FI.crv lh.sphere.reg rh.area.mid rh.inflated.K rh.pial-outer-smoothed rh.smoothwm.K2.crv rh.volume lh.inflated lh.piallh.smoothwm.H.crv lh.sulc rh.area.pialrh.jacobian_white rh.smoothwm rh.smoothwm.K.crv rh.w-g.pct.mgh Here's the entire output: -- [rimol @ ~/subjects/long/long_v0v2_amd]$ mris_preproc --qdec-long ~/long_qdec_FINAL2_w33_model1.dat --target fsaverage --hemi lh --meas area --area pial --out test_pial.mgh nsubjects = 172 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.11745 /cluster/home/rimol/subjects/long/long_v0v2_amd Log file is test_pial.mris_preproc.log Thu Sep 18 17:23:19 CEST 2014 setenv SUBJECTS_DIR /usit/abel/u1/rimol/subjects/long/long_v0v2_amd cd /cluster/home/rimol/subjects/long/long_v0v2_amd /cluster/software/VERSIONS/freesurfer-5.3.0/bin/mris_preproc --qdec-long /usit/abel/u1/rimol/long_qdec_FINAL2_w33_model1.dat --target fsaverage --hemi lh --meas area --area pial --out test_pial.mgh Linux login-0-1.local 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.11745 Src lh sphere.reg Trg lh sphere.reg --- #@# 1/172 007v2.long.007_base Thu Sep 18 17:23:19 CEST 2014 -- --- mri_surf2surf --srcsubject 007v2.long.007_base --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.11745/007v2.long.007_base.1.mgh --sval-area pial --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 007v2.long.007_base srcval = (null) srctype= curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.11745/007v2.long.007_base.1.mgh trgtype= srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.sphere.reg Loading source data Reading curvature file /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) MRISreadCurvature: could not open /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) No such file or directory ERROR: reading curvature file -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ 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] quick quality assessment for MPRAGE images
Hi Ezra, I'd love to hear otherwise if someone has established some robust signal processing approaches to do this automatically, but I'm not aware of any good reliable ways to do this in a automated fashion. It is time consuming, but you have to put eyes on the data. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Wegbreit, Ezra ezra_wegbr...@brown.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, September 18, 2014 9:56 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] quick quality assessment for MPRAGE images Dear Freesurfer Users, I have a large number of T1 MPRAGE scans collected on a 3T Siemens Trio scanner that I would like to run through recon-all to get cortical thickness values. However, some of the MPRAGE scans are contaminated by subject motion, but the extent of this varies from scan to scan. Is there a quick automated way to assess whether each MPRAGE is high-quality enough to bother with running through recon-all? Thanks! Ezra ___ Ezra Wegbreit, PhD NIMH T32 Post-doctoral Research Fellow in Child Mental Health Pedi-MIND Program at Bradley Hospital Department of Psychiatry and Human Behavior Brown University Medical School (401) 432-1615 ezra_wegbr...@brown.edu (preferred) ewegbr...@lifespan.org ___ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Scatter plot from mri_glmfit analyses
Hi Doug and FS team I did glm analyses using mri_glmfit, and I was trying to plot the individual values in the population for a specific significant cluster. However I am not sure how to extract individual values from the entire cluster. (note that the concatenated surface used as input for the glm contains some 0 values that I want to exclude from the mean value of the cluster). Is there a way to build a label from a specific significant cluster? Then, I was thinking about using mri_segstats --avgwf on the 4D concatenated file to get the average of the region but is there a way to not include 0 values? And then I was also interested in getting the correlation coefficient from that same cluster, so maybe the script below would be helpful for that but I could not open it. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_glm_pcc.m Thanks so much for your help Best Celine On 05/31/2012 06:09 AM, Knut J Bjuland wrote: Hi I am trying to calculate correlation coefficient using freesurfer GLM for associations between volumes and IQ. I found this ealier answar, but the matlab script but the link appear to be dead. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22648.html Best regards Knut J ___ 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 ___ 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] quick quality assessment for MPRAGE images
Try out Freesurfer's QAtools. It still isn't automatic, but you can get a bunch of screenshots and view them all on an html page. On 09/18/2014 11:42 AM, Harms, Michael wrote: Hi Ezra, I'd love to hear otherwise if someone has established some robust signal processing approaches to do this automatically, but I'm not aware of any good reliable ways to do this in a automated fashion. It is time consuming, but you have to put eyes on the data. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu From: Wegbreit, Ezra ezra_wegbr...@brown.edu mailto:ezra_wegbr...@brown.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Date: Thursday, September 18, 2014 9:56 AM To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] quick quality assessment for MPRAGE images Dear Freesurfer Users, I have a large number of T1 MPRAGE scans collected on a 3T Siemens Trio scanner that I would like to run through recon-all to get cortical thickness values. However, some of the MPRAGE scans are contaminated by subject motion, but the extent of this varies from scan to scan. Is there a quick automated way to assess whether each MPRAGE is high-quality enough to bother with running through recon-all? Thanks! Ezra *___* *Ezra Wegbreit, PhD* NIMH T32 Post-doctoral Research Fellow in Child Mental Health Pedi-MIND Program at Bradley Hospital Department of Psychiatry and Human Behavior Brown University Medical School (401) 432-1615 ezra_wegbr...@brown.edu mailto:ezra_wegbr...@brown.edu (preferred) ewegbr...@lifespan.org mailto:ewegbr...@lifespan.org *___* The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] quick quality assessment for MPRAGE images
Yes, that can be helpful. As a caution though, the overall quality may appear fine, but things like topology correction errors can still occur and will be quite local. Thus, they would easily be missed if the density of your screenshots isn't high enough. Personally, I find it only marginally more time consuming to navigate through the entire set of slices in 'tkmedit', and the quality of your QA will be better. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Chris Watson christopher.wat...@childrens.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, September 18, 2014 2:00 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] quick quality assessment for MPRAGE images Try out Freesurfer's QAtools. It still isn't automatic, but you can get a bunch of screenshots and view them all on an html page. On 09/18/2014 11:42 AM, Harms, Michael wrote: Hi Ezra, I'd love to hear otherwise if someone has established some robust signal processing approaches to do this automatically, but I'm not aware of any good reliable ways to do this in a automated fashion. It is time consuming, but you have to put eyes on the data. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Wegbreit, Ezra ezra_wegbr...@brown.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, September 18, 2014 9:56 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] quick quality assessment for MPRAGE images Dear Freesurfer Users, I have a large number of T1 MPRAGE scans collected on a 3T Siemens Trio scanner that I would like to run through recon-all to get cortical thickness values. However, some of the MPRAGE scans are contaminated by subject motion, but the extent of this varies from scan to scan. Is there a quick automated way to assess whether each MPRAGE is high-quality enough to bother with running through recon-all? Thanks! Ezra ___ Ezra Wegbreit, PhD NIMH T32 Post-doctoral Research Fellow in Child Mental Health Pedi-MIND Program at Bradley Hospital Department of Psychiatry and Human Behavior Brown University Medical School (401) 432-1615 ezra_wegbr...@brown.edu (preferred) ewegbr...@lifespan.org ___ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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
Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
When you look at SUBJECT_ID_CBF_reg.nii.gz, does it look reasonable? Does it overlay correctly on the T1.mgz? doug On 09/14/2014 11:40 PM, Salil Soman wrote: Thank you Doug. I am having trouble with extracting statistics using this method. I am able to use bbregister to get a transformation that registers the PD image of the ASL to the T1. I then used this transformation matrix to register the CBF map for the ASL study into the T1.mgz space. Checking the images, the registration looked reasonable. However, when I try to extract the values from the registered image using the vois from aparc+aseg.mgz, and the FreeSurferColorLUT I get all 0 values. *The command I ran is:* mri_segstats --seg $SUBJECTS_DIR/SUBJECT_ID/mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i SUBJECT_ID_CBF_reg.nii.gz --sum SUBJECT_ID_ASL.stats --seg-erode 1 *where SUBJECT_ID_CBF_reg.nii.gz was generated by running:* mri_vol2vol --mov SUBJECT_ID_CBF.nii.gz --targ T1.mgz --interp nearest --o SUBJECT_ID_CBF_reg.nii.gz --reg SUBJECT_ID.dat --no-save-reg (and this was run with T1.mgz and SUBJECT_ID_CBF.nii.gz in the same folder). *for which SUBJECT_ID.dat was generated by running the code:* bbregister --s SUBJECT_ID --mov SUBJECT_ID_ASL_PD.nii.gz --reg SUBJECT_ID.dat --t1 --init-fsl Thank you for your consideration of this question. Best wishes, Salil Soman, MD, MS On Sun, Sep 14, 2014 at 3:32 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: yep, you can use it for anything. doug On 9/14/14 12:52 PM, Salil Soman wrote: Dear Doug, Thank you again for this email. Do you think it is possible to use this method for ASL images as well? If so, how would you change the options? Best wishes, Salil Soman, MD, MS On Sat, May 25, 2013 at 11:51 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 5/25/13 1:39 PM, Salil Soman wrote: Thank you Doug. Just so I am clear - is the anatomical the nifti T1.mgz or is it a different file. From your email I gather should do the following: *1) Use bbregister to register the lowb image to the anatomical. This creates a registration matrix.* bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat That is right, but add --t2 (since it is t2 weighted). *2) Use mri_vol2vol and the registration to map the ADC map to the anatomical* mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff --reg $outdir/register.dat --no-save-reg Use the ADC as the moveable (not lowb, but use the lowb for bbregister). The target volume should be the T1.mgz (or any conformed volume). The output will be the adc in the anatomical space (not sure why you call it vol2diff). *3) use mri_segstats to extract the values* *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats The input would be the adc volume mapped the anatomical space. I would use WMParcStatsLUT.txt or else you'll get a billion different areas not represented in wmparc. You may also want to add --seg-erode 1 to erode the segmentations by a voxel. This helps to prevent partial voluming. doug Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. ADC), $vol2diff is the output image of the registration, and fa.stats will be my output stats table? I suspect there is part of the syntax for these tools I do not understand. Also, what input would $vol be? Best wishes, Sal On Sat, May 25, 2013 at 10:06 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Sal, yes you can. Use bbregister to register the lowb image to the anatomical. This creates a registration matrix. Use mri_vol2vol and the registration to map the ADC map to the anatomical, then use mri_segstats to extract the values doug ps. Please post questions to the FS list instead of us directly so that others can benefit and it gets archived. thanks! On 5/25/13 1:03 PM, Salil Soman wrote: Dear Dr. Greve, Is it possible to register a nonstructural MR sequences (e.g. an ADC map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, using the segmentation from the aseg (or aparc+aseg) file to output a mean ADC value for each anatomic area segmented? Thank you for
Re: [Freesurfer] mincost bb_register
0.5 is pretty good for fMRI. If it looks good visually, then I would not worry about it further doug On 09/17/2014 09:25 AM, lorenzo pasquini wrote: Dear Freesurfer users, I have used the command bb_register to automatically register raw fMRI data on the anatomy. The output looks visually fine, however the mincost file gives me values around 0.5 for my subjects. Is this range acceptable? Does anybody has a hint on how the registration could be optimized? I use init-fsl and --bold as contrast in my bbregister command. Best, Lorenzo ___ 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.
Re: [Freesurfer] Pial Surface Incorrect For Native T1
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.
Re: [Freesurfer] exporting QDEC results
The easiest way is to run mri_glmfit-sim from the command line on the QDEC output folder. It will automatically correct for multiple comparisons and create tables. See the tutorial (and other posts along this line). doug On 09/18/2014 05:56 AM, elisa veronese wrote: Dear FreeSurfers, can anybody tell me if there is a way to export results in form of table (or text file) from the QDEC GUI after having performed analysis on thickness, area, volume, etc etc... ? I mean, is the infomation regarding the significant clusters saved in table format? Thank you. Best, Elisa -- Elisa Veronese - PhD / Research Unit on Brain Imaging and Neuropsychology (RUBIN) / / Inter-University Center for Behavioral Neurosciences (ICBN) University of Udine and University of Verona, Italy / ICBN Website: http://icbn.uniud.it/tiki-index.php / / ___ 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.
Re: [Freesurfer] mri_vol2surf
For each vertex, the col, row, slice in the mdi is computed based on the registration. The value from this voxel is extracted; the default is nearest neighbor but this can be changed with --interp trilin doug On 09/18/2014 10:52 AM, Nicholas Heugel wrote: I looked over the documentation but can;t seem to find what I am looking for. How exactly does the function project the mdi data onto the surface? What method is it using to accomplish this, is it just projecting to the nearest neighbor or is there something more complex occurring. I ask because I just want to make sure I completely understand what every step in my analysis is doing and not have it be a blackbox that I put data in and it gives me stuff out. Thanks for your help. Nicholas ___ 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.
Re: [Freesurfer] problem with mris_preproc
This is a bug in mris_preproc. A work-around is to add --srcfmt mgh as the last argument. In the mean time I'll fix mris_preproc doug On 09/18/2014 11:32 AM, Lars M. Rimol wrote: Hi, I get the following error message when running mris_preproc, and I'm wondering what file is it looking for?: Reading curvature file /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) MRISreadCurvature: could not open /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) No such file or directory ERROR: reading curvature file This subject, 007, seems to have all the files it should: [rimol @ ~/subjects/long/long_v0v2_amd]$ ls /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf lh.area lh.inflated.H lh.pial_lgi lh.smoothwm.K1.crv lh.thicknessrh.avg_curv rh.orig rh.smoothwm.BE.crv rh.smoothwm.S.crv rh.white lh.area.mid lh.inflated.K lh.pial-outer-smoothed lh.smoothwm.K2.crv lh.volume rh.curv rh.orig_pial rh.smoothwm.C.crv rh.sphere lh.area.pial lh.jacobian_white lh.smoothwm lh.smoothwm.K.crv lh.w-g.pct.mgh rh.curv.pial rh.orig_white rh.smoothwm.FI.crv rh.sphere.reg lh.avg_curv lh.origlh.smoothwm.BE.crv lh.smoothwm.S.crv lh.whiterh.inflated rh.pial rh.smoothwm.H.crv rh.sulc lh.curv lh.orig_pial lh.smoothwm.C.crv lh.sphere rh.area rh.inflated.H rh.pial_lgi rh.smoothwm.K1.crv rh.thickness lh.curv.pial lh.orig_white lh.smoothwm.FI.crv lh.sphere.reg rh.area.mid rh.inflated.K rh.pial-outer-smoothed rh.smoothwm.K2.crv rh.volume lh.inflated lh.piallh.smoothwm.H.crv lh.sulc rh.area.pialrh.jacobian_white rh.smoothwm rh.smoothwm.K.crv rh.w-g.pct.mgh Here's the entire output: -- [rimol @ ~/subjects/long/long_v0v2_amd]$ mris_preproc --qdec-long ~/long_qdec_FINAL2_w33_model1.dat --target fsaverage --hemi lh --meas area --area pial --out test_pial.mgh nsubjects = 172 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.11745 /cluster/home/rimol/subjects/long/long_v0v2_amd Log file is test_pial.mris_preproc.log Thu Sep 18 17:23:19 CEST 2014 setenv SUBJECTS_DIR /usit/abel/u1/rimol/subjects/long/long_v0v2_amd cd /cluster/home/rimol/subjects/long/long_v0v2_amd /cluster/software/VERSIONS/freesurfer-5.3.0/bin/mris_preproc --qdec-long /usit/abel/u1/rimol/long_qdec_FINAL2_w33_model1.dat --target fsaverage --hemi lh --meas area --area pial --out test_pial.mgh Linux login-0-1.local 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 tmpdir is ./tmp.mris_preproc.11745 Src lh sphere.reg Trg lh sphere.reg --- #@# 1/172 007v2.long.007_base Thu Sep 18 17:23:19 CEST 2014 -- --- mri_surf2surf --srcsubject 007v2.long.007_base --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.11745/007v2.long.007_base.1.mgh --sval-area pial --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 007v2.long.007_base srcval = (null) srctype= curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.11745/007v2.long.007_base.1.mgh trgtype= srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.sphere.reg Loading source data Reading curvature file /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) MRISreadCurvature: could not open /usit/abel/u1/rimol/subjects/long/long_v0v2_amd/007v2.long.007_base/surf/lh.(null) No such file or directory ERROR: reading curvature file -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway ___ 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:
Re: [Freesurfer] Scatter plot from mri_glmfit analyses
Have you run mri_glmfit-sim? It will create labels (ie, annotations) of the clusters as well as run mri_segstats to get means in each cluster for each subject. Try that link now doug On 09/18/2014 12:15 PM, Celine Louapre wrote: Hi Doug and FS team I did glm analyses using mri_glmfit, and I was trying to plot the individual values in the population for a specific significant cluster. However I am not sure how to extract individual values from the entire cluster. (note that the concatenated surface used as input for the glm contains some 0 values that I want to exclude from the mean value of the cluster). Is there a way to build a label from a specific significant cluster? Then, I was thinking about using mri_segstats --avgwf on the 4D concatenated file to get the average of the region but is there a way to not include 0 values? And then I was also interested in getting the correlation coefficient from that same cluster, so maybe the script below would be helpful for that but I could not open it. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_glm_pcc.m Thanks so much for your help Best Celine On 05/31/2012 06:09 AM, Knut J Bjuland wrote: Hi I am trying to calculate correlation coefficient using freesurfer GLM for associations between volumes and IQ. I found this ealier answar, but the matlab script but the link appear to be dead. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22648.html Best regards Knut J ___ 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.
Re: [Freesurfer] displaying a single label from aparc in tksurfer
The only way I know is to break the annotation into labels (mri_annotation2label), then creating a new annotation with only the labels you want (mris_label2annot). If you only want one label, then you don't need to create a new annotation doug On 09/18/2014 03:11 PM, Maria Kharitonova wrote: Hi all, I would like make a figure where only 1 or 2 regions (labels from the aparc.a2009s atlas are displayed). I know how to turn on/off all labels, but how do I only display 1? (e.g. rh_G_and_S_cingul-Mid-Ant). Turning off all but the one I need is tedious and I was wondering if there was a better way. I was able to change the color of the ACC region I needed to make it more apparent (see attached), but was looking for a way that the white region is only label that is shown. I looked through the archives but could not find anything. Thanks in advance for the help! Best, Maria -- Maria Kharitonova, PhD Research Assistant Professor Department of Medical Social Sciences Northwestern University Feinberg School of Medicine 625 N. Michigan Ave, Suite 2700 Chicago, IL 60611 Phone: (312) 503-6503 Email: maria.khariton...@northwestern.edu mailto:maria.khariton...@northwestern.edu ___ 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.
Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
Dear Doug, Thank you for your email. The registration overlap looks reasonable. Thank you for considering this question. Best wishes, Sal On Thu, Sep 18, 2014 at 12:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: When you look at SUBJECT_ID_CBF_reg.nii.gz, does it look reasonable? Does it overlay correctly on the T1.mgz? doug On 09/14/2014 11:40 PM, Salil Soman wrote: Thank you Doug. I am having trouble with extracting statistics using this method. I am able to use bbregister to get a transformation that registers the PD image of the ASL to the T1. I then used this transformation matrix to register the CBF map for the ASL study into the T1.mgz space. Checking the images, the registration looked reasonable. However, when I try to extract the values from the registered image using the vois from aparc+aseg.mgz, and the FreeSurferColorLUT I get all 0 values. *The command I ran is:* mri_segstats --seg $SUBJECTS_DIR/SUBJECT_ID/mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i SUBJECT_ID_CBF_reg.nii.gz --sum SUBJECT_ID_ASL.stats --seg-erode 1 *where SUBJECT_ID_CBF_reg.nii.gz was generated by running:* mri_vol2vol --mov SUBJECT_ID_CBF.nii.gz --targ T1.mgz --interp nearest --o SUBJECT_ID_CBF_reg.nii.gz --reg SUBJECT_ID.dat --no-save-reg (and this was run with T1.mgz and SUBJECT_ID_CBF.nii.gz in the same folder). *for which SUBJECT_ID.dat was generated by running the code:* bbregister --s SUBJECT_ID --mov SUBJECT_ID_ASL_PD.nii.gz --reg SUBJECT_ID.dat --t1 --init-fsl Thank you for your consideration of this question. Best wishes, Salil Soman, MD, MS On Sun, Sep 14, 2014 at 3:32 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: yep, you can use it for anything. doug On 9/14/14 12:52 PM, Salil Soman wrote: Dear Doug, Thank you again for this email. Do you think it is possible to use this method for ASL images as well? If so, how would you change the options? Best wishes, Salil Soman, MD, MS On Sat, May 25, 2013 at 11:51 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 5/25/13 1:39 PM, Salil Soman wrote: Thank you Doug. Just so I am clear - is the anatomical the nifti T1.mgz or is it a different file. From your email I gather should do the following: *1) Use bbregister to register the lowb image to the anatomical. This creates a registration matrix.* bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat That is right, but add --t2 (since it is t2 weighted). *2) Use mri_vol2vol and the registration to map the ADC map to the anatomical* mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff --reg $outdir/register.dat --no-save-reg Use the ADC as the moveable (not lowb, but use the lowb for bbregister). The target volume should be the T1.mgz (or any conformed volume). The output will be the adc in the anatomical space (not sure why you call it vol2diff). *3) use mri_segstats to extract the values* *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats The input would be the adc volume mapped the anatomical space. I would use WMParcStatsLUT.txt or else you'll get a billion different areas not represented in wmparc. You may also want to add --seg-erode 1 to erode the segmentations by a voxel. This helps to prevent partial voluming. doug Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. ADC), $vol2diff is the output image of the registration, and fa.stats will be my output stats table? I suspect there is part of the syntax for these tools I do not understand. Also, what input would $vol be? Best wishes, Sal On Sat, May 25, 2013 at 10:06 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Sal, yes you can. Use bbregister to register the lowb image to the anatomical. This creates a registration matrix. Use mri_vol2vol and the registration to map the ADC map to the anatomical, then use mri_segstats to extract the values doug ps. Please post questions to the FS list instead of us directly so that others can benefit and it gets archived. thanks! On 5/25/13 1:03 PM, Salil Soman wrote: Dear Dr. Greve, Is it possible to register a nonstructural MR sequences (e.g. an ADC map) with the aseg.mgz file (or
Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
Are you sure that *all* are 0? By passing it FreeSurferColorLUT.txt, you force it to report hundreds (or thousands) of ROIs which are not represented in the aparc+aseg.mgz. Also, try removing --seg-erode. On 09/18/2014 04:43 PM, Salil Soman wrote: Dear Doug, Thank you for your email. The registration overlap looks reasonable. Thank you for considering this question. Best wishes, Sal On Thu, Sep 18, 2014 at 12:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: When you look at SUBJECT_ID_CBF_reg.nii.gz, does it look reasonable? Does it overlay correctly on the T1.mgz? doug On 09/14/2014 11:40 PM, Salil Soman wrote: Thank you Doug. I am having trouble with extracting statistics using this method. I am able to use bbregister to get a transformation that registers the PD image of the ASL to the T1. I then used this transformation matrix to register the CBF map for the ASL study into the T1.mgz space. Checking the images, the registration looked reasonable. However, when I try to extract the values from the registered image using the vois from aparc+aseg.mgz, and the FreeSurferColorLUT I get all 0 values. *The command I ran is:* mri_segstats --seg $SUBJECTS_DIR/SUBJECT_ID/mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i SUBJECT_ID_CBF_reg.nii.gz --sum SUBJECT_ID_ASL.stats --seg-erode 1 *where SUBJECT_ID_CBF_reg.nii.gz was generated by running:* mri_vol2vol --mov SUBJECT_ID_CBF.nii.gz --targ T1.mgz --interp nearest --o SUBJECT_ID_CBF_reg.nii.gz --reg SUBJECT_ID.dat --no-save-reg (and this was run with T1.mgz and SUBJECT_ID_CBF.nii.gz in the same folder). *for which SUBJECT_ID.dat was generated by running the code:* bbregister --s SUBJECT_ID --mov SUBJECT_ID_ASL_PD.nii.gz --reg SUBJECT_ID.dat --t1 --init-fsl Thank you for your consideration of this question. Best wishes, Salil Soman, MD, MS On Sun, Sep 14, 2014 at 3:32 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: yep, you can use it for anything. doug On 9/14/14 12:52 PM, Salil Soman wrote: Dear Doug, Thank you again for this email. Do you think it is possible to use this method for ASL images as well? If so, how would you change the options? Best wishes, Salil Soman, MD, MS On Sat, May 25, 2013 at 11:51 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 5/25/13 1:39 PM, Salil Soman wrote: Thank you Doug. Just so I am clear - is the anatomical the nifti T1.mgz or is it a different file. From your email I gather should do the following: *1) Use bbregister to register the lowb image to the anatomical. This creates a registration matrix.* bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat That is right, but add --t2 (since it is t2 weighted). *2) Use mri_vol2vol and the registration to map the ADC map to the anatomical* mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff --reg $outdir/register.dat --no-save-reg Use the ADC as the moveable (not lowb, but use the lowb for bbregister). The target volume should be the T1.mgz (or any conformed volume). The output will be the adc in the anatomical space (not sure why you call it vol2diff). *3) use mri_segstats to extract the values* *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats The input would be the adc volume mapped the anatomical space. I would use WMParcStatsLUT.txt or else you'll get a billion different areas not represented in
Re: [Freesurfer] displaying a single label from aparc in tksurfer
Hi Maria, You can display a single label (or labels) in tksurfer by loading the aparc annotation onto fsaverage; then, simply click on the label you're interested in, and click File, then Label, and Save Selected Label. This will let you save out a single label from aparc, which can these easily be loaded onto fsaverage on its own. You can of course also overlay multiple labels in tksurfer that you've saved out in this way (and naturally change colour schemes if you're so inclined). Best, Dan --- On 18 Sep 2014, at 22:03, freesurfer-requ...@nmr.mgh.harvard.edu wrote: displaying a single label from aparc in tksurfer Daniel Carey Marie Curie Ph.D. Fellow, Centre for Brain and Cognitive Development, 32 Torrington Sq., London WC1E 7HX email: d.ca...@bbk.ac.uk web: http://www.cbcd.bbk.ac.uk/people/students/daniel_carey ___ 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] Map both hemisphere to lh of fsaverage_sym
Dear FreeSurfers, I have data has been recon-all analyzed. I would like to compare the symmetry of function/structure property between LH and RH, such as cortical thickness. I already know that the vertices in the left hemisphere are not correspond to vertices in the right hemisphere. I would like to know the exactly symmetric vertex for both hemisphere. Thus the question is, how can I register both hemisphere to one hemisphere of fsaverage_sym, then compare them? I followed the instruction: xhemireg --s sub001 surfreg --s sub001--t fsaverage_sym --lh surfreg --s sub001/xhemi --t fsaverage_sym --lh --xhemi then here is the error: MRISread(/data/sub001/xhemi/xhemi/surf/lh.sphere): could not open file No such file or directory mris_register: could not read surface file /data/sub001/xhemi/xhemi/surf/lh.sphere No such file or directory Thank you in advance for any suggestion! Regards, Ting ___ 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.
