Re: [Freesurfer] pial and WM missing after reunning skullstrip
Hi Julia, After the skull strip was corrected, you should run: recon-all -autorecon2 -autorecon3 -s Subject_name this will create new surfaces based on new skull strip. Tanja. On Mon, Aug 22, 2011 at 6:47 AM, Julia Hill julia.h...@neura.edu.au wrote: Hi Bruce I am new to freesurfer and im having a few issues with a number of my scans. The cerebellum and sections of the occipital lobe seems to be cut off on a number of subjects, so i went in and altered the skull stripping by increasing the watershed threshold to 35 and using -no-wsgcaatlas. When i review the scans afterwards, the pial and WM surfaces haven't included the original missing sections of the scans. How do i go back and include these missing sections? I have attached a screenshots. Thank you kindly Julia Julia Hill Research Assistant School of Psychiatry University of New South Wales Previously Prince of Wales Medical Research Institute www.NeuRA.edu.au http://neura.edu.au/ Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia *T *+61 2 9399 1268 ___ 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] DOSS or DODS
Hello Douglas, I did as you suggested and I got the results, but I still have difficulty understanding how exactly the choice of Design Matrix Type influences the analysis, so I have several questions: 1. When I look at thickness difference between two groups and choose age as nuisance parameter, doesn't it mean that calculation take into account the difference in slopes already (as I correct for age)? So therefore, when I also choose DODS or DOSS I do kind of double correction (matrix type + nuisance), don't I? 2. When I choose e.g. DODS and do the analysis, can I see the slopes (or the values of slopes) for two groups somehow? In which file this output is? 3. Can you recommend me anything to read regarding mathematics of how the analysis is done with either matrix type? 4. Just in case you know: how is this step implemented in SPM? It also uses glm, but it doesn't ask for the DODS vs DOSS choice. Thank you, I appreciate you time and help, Tanja. On Wed, Aug 17, 2011 at 6:19 PM, Tetiana Dadakova tetian...@gmail.com wrote: Thank you, Douglas. On Wed, Aug 17, 2011 at 5:48 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Tanja, you should use DODS and test for a difference between the age slopes of the groups (ie, an interaction between group and age). If there are no significant interactions, you should then use DOSS to test for the difference between thicknesses. doug Tetiana Dadakova wrote: Dear all, I have two groups of subjects, and I want to see a difference in thickness between them controlling for age. I couldn't find any information in the literature on how the subject's brains in my groups develop with age. Therefore I can't tell whether thickness as a function of age for both groups has the same slope or different. My question is if in this case I should use DODS? Thank you, Tanja. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] GLM or Qdec ?
Dear FS experts, I finished running the GLM and I wonder what is the best way to further analyse my data in order to see if there is any relation between age (at seizure onset) and cortical thickness for my patients versus control group. 1). Why when I overlay the sig.mgh in tksurfer lh inflated, I get more clusters than the number of clusters obtained from mri_glmfit-sim? 2). What sig.mgh represents? 3) What's the real significance of a cluster (how a cluster is formed)? 4). Why my thickness value in clusters (eg cluster no. 1 which coresponds to the posteriorcingulate) for subject no.1 is different that the thickness value obtained for the same region in the lh.aparc.stats while running recon-all? 5). After running the GLM should I use visualizing and plotting method to further analyse my data and load FSGD file lh.gender_age.glmdir/y.fsgd? 6). Should my ROI's be defined or be the same with my clusters? 7). What is the difference between GLM and Qdec? What method is the best to analyse the relation between age and cortical thickness for my patients versus control group? 8). Why when analysing with Qdec I get more clusters? Are this defining or representing the sig.mgh as in GLM? 9). When using Qdec were I can find as an output of results the number of clusters and the cortical thickness value? Thank you and have a great day! Antonella___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] FW: Occipital Flattening
Dear all,
I tried to cut the occiput surface with Freesurfer. When I follow the manual on
the Wikipage and description found here http://www.alivelearn.net/?cat=10 (Line
cut trough the calcarine sulcus, surface cut placing 2 points on the medial
side, 1 on the lateral side and a fourth point to specify which part I want to
keep) I get the following error when clicking the 'cut surface' button:
surfer: poffset = 205895.00, sign = 165453.718750, n =
{-703.239014,-3109.317627,-1290.049561}
% tksurfer.bin: tnl/t_vertex.c:407: update_input_ptrs: Assertion
`a[j].inputstride == vptr-stride' failed.
Aborted
Please could you help me with this problem?
Thank you in advance,
Kind regards,
Chantal
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[Freesurfer] GLM or Qdec
Dear FS experts, I finished running the GLM and I wonder what is the best way to further analyse my data in order to see if there is any relation between age (at seizure onset) and cortical thickness for my patients versus control group. 1). Why when I overlay the sig.mgh in tksurfer lh inflated, I get more clusters than the number of clusters obtained from mri_glmfit-sim? 2). What sig.mgh represents? 3) What's the real significance of a cluster (how a cluster is formed)? 4). Why my thickness value in clusters (eg cluster no. 1 which coresponds to the posteriorcingulate) for subject no.1 is different that the thickness value obtained for the same region in the lh.aparc.stats while running recon-all? 5). After running the GLM should I use visualizing and plotting method to further analyse my data and load FSGD file lh.gender_age.glmdir/y.fsgd? 6). Should my ROI's be defined or be the same with my clusters? 7). What is the difference between GLM and Qdec? What method is the best to analyse the relation between age and cortical thickness for my patients versus control group? 8). Why when analysing with Qdec I get more clusters? Are this defining or representing the sig.mgh as in GLM? 9). When using Qdec were I can find as an output of results the number of clusters and the cortical thickness value? Thank you and have a great day! Antonella___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Coordinate transformations from orig/001.mgz to T1.mgz
Hi Tommi, have you looked at this document? http://www.freesurfer.net/fswiki/CoordinateSystems?action=AttachFiledo=gettarget=fscoordinates.pdf doug r...@nmr.mgh.harvard.edu wrote: Hi, We (Aapo Nummenmaa and I) are developing cross-platform software that would allow translating third-party coordinates back and forth with Freesurfer segmentations. Our example structural image is MEMPRAGE_4e_p2_1mm_iso (1 mm isotropic, 192 sagittal slices, T1 weighting). Our third-party system (TMS-navigator Nexstim NBS) uses DICOM/nifti with origin (0,0,0) at right posterior inferior corner of the stack with x=R-L y=I-S z=P-A. Our goal is to relate the Nexstim NBS coordinates to these two images: 1. $SUBJECTS_DIR/$SUBJECT/mri/orig/001.mgz (not altered by recon-all) 2. $SUBJECTS_DIR/$SUBJECT/mri/T1.mgz (altered by recon-all) For (1) above, Volume Index in tkmedit looks like this: origin (0,0,0) is at right anterior superior corner of the stack with x=A-P y=S-I z=R-L. Max values in tkmedit display were (255,243,191). The acquisition had 192 sagittal slices so the last number makes sense - not sure why the second figure is not 255 (perhaps just a display thing). The orig/001.mgz stack should be exactly the same stack as in the Nexstim NBS image (which is just the plain DICOM), without any resampling or other processing, just the axes have been reshuffled a bit. For (2) above, Volume Index in tkmedit looks like this: origin (0,0,0) is at right posterior superior corner of the stack with x=R-L y=S-I z=P-A. Max values in tkmedit display were (255,255,255). This makes things difficult, as we do not know what exactly recon-all did to orig/001.mgz when it converted it into T1.mgz. Our question is this: Is there a deterministic way to go from orig/001.mgz to T1.mgz Volume Index coordinates? It seems that recon-all has at least added sagittal slices to make the T1.mgz stack into a cube (looking at lateral shift between 001.mgz and T1.mgz, I would guess that 32 1-mm slices on both sides (2*32+192=256) were added)... Further, it is not clear if the orig/001.mgz volume has been shifted, rotated, or resampled by recon-all when turning it into T1.mgz. Thank you for the advice! Bests, Tommi Aapo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Avg.Thickness in a cluster
Does cluster cover the exact same region in the group map as in the individual? Even if you choose the same nominal region (eg, posterior cingulate) you will not get the same exact number when you do it in fsaverage space as when it is done in the native space. doug Antonella Kis wrote: Dear Doug, I just checked my results for the average thickness from each subject generated in the csdbase.y.ocn.dat file in different clusters (e.g. I have 5 clusters for p0.05). For cluster #1 - posteriorcingulate, the average thickness for subject 1 is different from the average thickness value in the same region-posteriorcingulate, in the lh.aparc.stats for the same subject. I thought it should be the same. Why they are different? Is this right? MANY THANKS! Antonella -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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_glmfit-sim
You should run mri_glmfit-sim as described in the tutorial and slides on line. This will correct for multiple comparisons. You can report the clusters that survive (if any). doug Antonella Kis wrote: Dear Doug, I will be very grateful if you can advise me with the following issue: if I finished running the GLM what is the best way to further analyse my data in order to see if there is any relation between age (at seizure onset) and cortical thickness for my patients versus control group. Should I check only within the formed clusters? How should analyse my data after completing the GLM? Should I use visualize and plotting and in this case should I load the clusters as my ROI? I am very confused and I have no clue how to further analyse my data. THANK YOU VERY MUCH! Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Sent:* Thursday, August 18, 2011 1:09 PM *Subject:* Re: [Freesurfer] mri_glmfit-sim No you don't. This is the reason I wrote mri_glmfit-sim -- so you don't need to specify things that it can figure out automatically. doug Antonella Kis wrote: Hi Doug, When I run the: mri_glmfit-sim \ --glmdir lh.age.glmdir \ --cache 4 neg \ --overwrite do I need to specify the --fwhm and/or to use the residual fwhm obtained from the y.fsgd file? If not when I have to input this value during my GLM analysis? Thank you. Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com mailto:ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, August 17, 2011 1:10 PM *Subject:* Re: [Freesurfer] mri_glmfit-sim Antonella Kis wrote: Hi Doug, Thanks again for your help. There are few more things not very clear for me and I will be very graetful if you can advise me: 1). Did you mean that if I did not qcache my data while I was doing pre-processing running the recon-all I should use then lh.AGE.thickness.10B.mgh? yes 2) Are then the mentioned steps the right one to be followed? yes 3) I saw on one tutorial about the mri_glm to perform estimations. What are this estimations? Do I need to run: Where did you see reference to mris_glm? This is an old program that we should not even distribute. # For the left hemisphere mris_glm --surfmeas thickness \ --hemi lh \ --trgsubj average \ --fsgd ./my_gender_age_fsgd.txt doss \ --beta ./beta_doss-thickness-100lh.mgz\ --var ./var_doss-thickness-100lh.mgz \ --y ./y_doss-thickness-100lh_000.mgz \ --nsmooth 100 # For the right hemisphere mris_glm --surfmeas thickness \ --hemi rh \ --trgsubj average \ --fsgd ./my_gender_age_fsgd.txt doss \ --beta ./beta_doss-thickness-100rh.mgz \ --var ./var_doss-thickness-100rh.mgz \ --y ./y_doss-thickness-100rh_000.mgz \ --nsmooth 100 4) If I have less than 80 subjects do I need to run the full MC simulation and I must supply the smoothest of my data as fwhm from the y.fsgd file? Also I would need to mention the threshold like in the following example? Yes. You are better off using mri_glmfit-sim rather than the command line below. mri_glmfit-sim will run that program giving it the appropriate fwhm. mri_glmfit --y lh.gender_age.thickness.10.mgh \ --glmdir lh.gender_age.glmdir \ --fsgd gender_age.txt doss \ --surf fsaverage lh \ --fwhm 14.517 --C age.mat \ --sim mc-full 1 2 lh.gender_age.glmdir/csd1 Do I add the --cache 4 neg \ --overwrite at the end? 5) When I run tksurfer to view the sig.mgh file and I set the threshold to 2, meaning vertices with p.01, I have just few vertices coloured in blue. Does this mean a low activation? If yes, what I have to do? Yes. You can try lowering it to 1.3 (p.05). If the effect is too subtle, you will need to add more subjects (assuming there is an effect at all). doug Thank you very much! Antonella *From:* Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *To:* Antonella Kis ator...@yahoo.com mailto:ator...@yahoo.com mailto:ator...@yahoo.com mailto:ator...@yahoo.com *Cc:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
[Freesurfer] V1 on fsaverage
Hi Is it possible to estimate the V1 boundary on fsaverage using Hinds method ? Thanks Ri ___ 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] Transforming freesurfer meshes to FSL coordinates
Todd, have you looked at our documentation on coordinate systems? http://www.freesurfer.net/fswiki/CoordinateSystems?action=AttachFiledo=gettarget=fscoordinates.pdf This gives the relationship between the FS and FSL coords doug Todd Krieg wrote: I am trying to use the output meshes from freesurfer (lh/rh.pial and lh/rh.white converted to .stl) with the BET meshes from FSL. They seem to be in different coordinate systems and have to be moved and scaled to match correctly. Is there an easy transform that can do this. I have tried several with no success. ---Todd Krieg Illinois Institute of Technology ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] DOSS or DODS
For question #3; #4. #3 Any good stastistical textbook will be useful. The two that come to mind are: (a) Meyers and Wells. Research Design and Statistical A nalysis (b) Keppel and Wickens. Design and Analysis: A Researcher's Handbook (4th Edition) #4 SPM uses the General Linear Model for all of its second level models. The DODS and DOSS are terms used in the freesurfer package and not in other packages; however, the designs can easily be generated in SPM. DODS -- Design matrix with different slopes per group Select two-sample t-test (or flexible factorial) Specify your two groups of scans Specify the covariate values, names, and select interaction with factor 1 You can ask if the slopes are different DOSS -- Design matrix with same slopes across all groups Select two-sample t-test (or flexible factorial) Specify your two groups of scans Specify the covariate values, names, and select interaction none. The slopes are modelled as a single regressor, so you can't ask about the difference in slopes between groups. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Mon, Aug 22, 2011 at 8:46 AM, Tetiana Dadakova tetian...@gmail.comwrote: Hello Douglas, I did as you suggested and I got the results, but I still have difficulty understanding how exactly the choice of Design Matrix Type influences the analysis, so I have several questions: 1. When I look at thickness difference between two groups and choose age as nuisance parameter, doesn't it mean that calculation take into account the difference in slopes already (as I correct for age)? So therefore, when I also choose DODS or DOSS I do kind of double correction (matrix type + nuisance), don't I? 2. When I choose e.g. DODS and do the analysis, can I see the slopes (or the values of slopes) for two groups somehow? In which file this output is? 3. Can you recommend me anything to read regarding mathematics of how the analysis is done with either matrix type? 4. Just in case you know: how is this step implemented in SPM? It also uses glm, but it doesn't ask for the DODS vs DOSS choice. Thank you, I appreciate you time and help, Tanja. On Wed, Aug 17, 2011 at 6:19 PM, Tetiana Dadakova tetian...@gmail.com wrote: Thank you, Douglas. On Wed, Aug 17, 2011 at 5:48 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Tanja, you should use DODS and test for a difference between the age slopes of the groups (ie, an interaction between group and age). If there are no significant interactions, you should then use DOSS to test for the difference between thicknesses. doug Tetiana Dadakova wrote: Dear all, I have two groups of subjects, and I want to see a difference in thickness between them controlling for age. I couldn't find any information in the literature on how the subject's brains in my groups develop with age. Therefore I can't tell whether thickness as a function of age for both groups has the same slope or different. My question is if in this case I should use DODS? Thank you, Tanja. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 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
Re: [Freesurfer] Coordinate transformations from orig/001.mgz to T1.mgz
Do you just need a vox2vox that goes from the conformed space back to the original dicom space? That's pretty easy, if that's the case. doug Aapo Nummenmaa wrote: Hi Doug, thanks for the reply. I have looked at the document and know approximately how things are defined. Our target TMS coordinate system is defined in terms of the original DICOM data and is LSA, independent of how the data was acquired (let's say it is PIL). I know naturally how to go from PIL to RAS to LSA and so forth within this volume. I operate with MATLAB, so when I load this stuff in, I can see if the column-row-slice order actually is LIA, PIL or whatnot mri_info says. But once the original data is processed by FS, to my understanding the data is conformed to be isotropic 1 mm voxels with matrix 256x256x256 and orientation LIA. So Tommi's question is can we incorporate this resampling procedure to obtain some kind of voxel-to-voxel transformation directly. It should be straightforward in principle, but I'm not sure what FreeSurfer exactly does during this resampling step. Assuming isotropic 1mm voxels to begin with, it seems to zero-fill the volume keeping the center of the FOV fixed. For now, I have just reverse engineered the voxel to voxel (or rather XYZ to XYZ) transformation by identifying same anatomical landmarks in the TMS and FreeSurfer coordinates. I guess we can also use bbregister to co-register the original data with orig.mgz (or T1.mgz) as an /ad hoc /solution. But of course, as Tommi pointed out, if the transformation can be figured out directly, that would be the nicest option. Thanks, -Aapo On Aug 22, 2011, at 11:55 AM, Douglas N Greve wrote: Hi Tommi, have you looked at this document? http://www.freesurfer.net/fswiki/CoordinateSystems?action=AttachFiledo=gettarget=fscoordinates.pdf http://www.freesurfer.net/fswiki/CoordinateSystems?action=AttachFiledo=gettarget=fscoordinates.pdf doug r...@nmr.mgh.harvard.edu wrote: Hi, We (Aapo Nummenmaa and I) are developing cross-platform software that would allow translating third-party coordinates back and forth with Freesurfer segmentations. Our example structural image is MEMPRAGE_4e_p2_1mm_iso (1 mm isotropic, 192 sagittal slices, T1 weighting). Our third-party system (TMS-navigator Nexstim NBS) uses DICOM/nifti with origin (0,0,0) at right posterior inferior corner of the stack with x=R-L y=I-S z=P-A. Our goal is to relate the Nexstim NBS coordinates to these two images: 1. $SUBJECTS_DIR/$SUBJECT/mri/orig/001.mgz (not altered by recon-all) 2. $SUBJECTS_DIR/$SUBJECT/mri/T1.mgz (altered by recon-all) For (1) above, Volume Index in tkmedit looks like this: origin (0,0,0) is at right anterior superior corner of the stack with x=A-P y=S-I z=R-L. Max values in tkmedit display were (255,243,191). The acquisition had 192 sagittal slices so the last number makes sense - not sure why the second figure is not 255 (perhaps just a display thing). The orig/001.mgz stack should be exactly the same stack as in the Nexstim NBS image (which is just the plain DICOM), without any resampling or other processing, just the axes have been reshuffled a bit. For (2) above, Volume Index in tkmedit looks like this: origin (0,0,0) is at right posterior superior corner of the stack with x=R-L y=S-I z=P-A. Max values in tkmedit display were (255,255,255). This makes things difficult, as we do not know what exactly recon-all did to orig/001.mgz when it converted it into T1.mgz. Our question is this: Is there a deterministic way to go from orig/001.mgz to T1.mgz Volume Index coordinates? It seems that recon-all has at least added sagittal slices to make the T1.mgz stack into a cube (looking at lateral shift between 001.mgz and T1.mgz, I would guess that 32 1-mm slices on both sides (2*32+192=256) were added)... Further, it is not clear if the orig/001.mgz volume has been shifted, rotated, or resampled by recon-all when turning it into T1.mgz. Thank you for the advice! Bests, Tommi Aapo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
Re: [Freesurfer] Coordinate transformations from orig/001.mgz to T1.mgz
Yeah, that should be enough. Basically it is just a coordinate shift, then? I can (probably) figure out remaining part of the transformation to the TMS system. By the way, when I use mri_info --vox2ras-tkr on the original data (which is PIL), does it give me the vox2ras on the conformed (LIA) or the original (PIL) coordinate system? I would guess the conformed? Thanks, -Aapo On Aug 22, 2011, at 2:06 PM, Douglas N Greve wrote: Do you just need a vox2vox that goes from the conformed space back to the original dicom space? That's pretty easy, if that's the case. doug Aapo Nummenmaa wrote: Hi Doug, thanks for the reply. I have looked at the document and know approximately how things are defined. Our target TMS coordinate system is defined in terms of the original DICOM data and is LSA, independent of how the data was acquired (let's say it is PIL). I know naturally how to go from PIL to RAS to LSA and so forth within this volume. I operate with MATLAB, so when I load this stuff in, I can see if the column-row-slice order actually is LIA, PIL or whatnot mri_info says. But once the original data is processed by FS, to my understanding the data is conformed to be isotropic 1 mm voxels with matrix 256x256x256 and orientation LIA. So Tommi's question is can we incorporate this resampling procedure to obtain some kind of voxel-to-voxel transformation directly. It should be straightforward in principle, but I'm not sure what FreeSurfer exactly does during this resampling step. Assuming isotropic 1mm voxels to begin with, it seems to zero-fill the volume keeping the center of the FOV fixed. For now, I have just reverse engineered the voxel to voxel (or rather XYZ to XYZ) transformation by identifying same anatomical landmarks in the TMS and FreeSurfer coordinates. I guess we can also use bbregister to co-register the original data with orig.mgz (or T1.mgz) as an /ad hoc /solution. But of course, as Tommi pointed out, if the transformation can be figured out directly, that would be the nicest option. Thanks, -Aapo On Aug 22, 2011, at 11:55 AM, Douglas N Greve wrote: Hi Tommi, have you looked at this document? http://www.freesurfer.net/fswiki/CoordinateSystems?action=AttachFiledo=gettarget=fscoordinates.pdf http://www.freesurfer.net/fswiki/CoordinateSystems?action=AttachFiledo=gettarget=fscoordinates.pdf doug r...@nmr.mgh.harvard.edu wrote: Hi, We (Aapo Nummenmaa and I) are developing cross-platform software that would allow translating third-party coordinates back and forth with Freesurfer segmentations. Our example structural image is MEMPRAGE_4e_p2_1mm_iso (1 mm isotropic, 192 sagittal slices, T1 weighting). Our third-party system (TMS-navigator Nexstim NBS) uses DICOM/nifti with origin (0,0,0) at right posterior inferior corner of the stack with x=R-L y=I-S z=P-A. Our goal is to relate the Nexstim NBS coordinates to these two images: 1. $SUBJECTS_DIR/$SUBJECT/mri/orig/001.mgz (not altered by recon-all) 2. $SUBJECTS_DIR/$SUBJECT/mri/T1.mgz (altered by recon-all) For (1) above, Volume Index in tkmedit looks like this: origin (0,0,0) is at right anterior superior corner of the stack with x=A-P y=S-I z=R-L. Max values in tkmedit display were (255,243,191). The acquisition had 192 sagittal slices so the last number makes sense - not sure why the second figure is not 255 (perhaps just a display thing). The orig/001.mgz stack should be exactly the same stack as in the Nexstim NBS image (which is just the plain DICOM), without any resampling or other processing, just the axes have been reshuffled a bit. For (2) above, Volume Index in tkmedit looks like this: origin (0,0,0) is at right posterior superior corner of the stack with x=R-L y=S-I z=P-A. Max values in tkmedit display were (255,255,255). This makes things difficult, as we do not know what exactly recon-all did to orig/001.mgz when it converted it into T1.mgz. Our question is this: Is there a deterministic way to go from orig/001.mgz to T1.mgz Volume Index coordinates? It seems that recon-all has at least added sagittal slices to make the T1.mgz stack into a cube (looking at lateral shift between 001.mgz and T1.mgz, I would guess that 32 1-mm slices on both sides (2*32+192=256) were added)... Further, it is not clear if the orig/001.mgz volume has been shifted, rotated, or resampled by recon-all when turning it into T1.mgz. Thank you for the advice! Bests, Tommi Aapo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- Douglas N. Greve, Ph.D.
Re: [Freesurfer] GLM or Qdec ?
Antonella Kis wrote: Dear FS experts, I finished running the GLM and I wonder what is the best way to further analyse my data in order to see if there is any relation between age (at seizure onset) and cortical thickness for my patients versus control group. 1). Why when I overlay the sig.mgh in tksurfer lh inflated, I get more clusters than the number of clusters obtained from mri_glmfit-sim? When you look at it in tksurfer, you are looking at uncorrected data. glmfit-sim corrects for multiple comparisons. Some of the clusters don't survive. 2). What sig.mgh represents? -log10(p) 3) What's the real significance of a cluster (how a cluster is formed)? It is based on the likelihood of getting a cluster of that size by chance given the search space (cortical surface area), smoothness (FWHM), and cluster-forming threshold (eg, p.05). 4). Why my thickness value in clusters (eg cluster no. 1 which coresponds to the posteriorcingulate) for subject no.1 is different that the thickness value obtained for the same region in the lh.aparc.stats while running recon-all? 5). After running the GLM should I use visualizing and plotting method to further analyse my data and load FSGD file lh.gender_age.glmdir/y.fsgd? 6). Should my ROI's be defined or be the same with my clusters? I don't know what you mean by that. 7). What is the difference between GLM and Qdec? What method is the best to analyse the relation between age and cortical thickness for my patients versus control group? They are the same statistically. They are just different ways to provide information about your design and contrasts. QDEC is graphical (point and click). mri_glmfit you create FSGD files and run it from the command-line. QDEC actually creates FSGD files and contrast files and runs mri_glmfit. 8). Why when analysing with Qdec I get more clusters? Are this defining or representing the sig.mgh as in GLM? They should give identical results when run in the same way. My guess is that you have created two different designs and so are getting different answers. 9). When using Qdec were I can find as an output of results the number of clusters and the cortical thickness value? You'll have to run the correction for multiple comparisons (interface on the results page). This simply runs mri_glmfit-sim. doug Thank you and have a great day! Antonella ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Unusual findings in regression analyses
Hi Adam, I see what you mean. In looking at your stimulus schedules (slopepar and paradigm), there seems to be an in consistency in the timing. Eg, in paradigm there is a stimulus at t=25, but the closest stimuli in slopepar are at t=23.62 and t=26.35. Can you resolve this for me? doug Adam Nitenson wrote: Hi Doug, We've been running a regression analysis on our subjects, and the results are quite puzzling as they don't seem to sync up with the individual pieces of the regression. The data is taken from the Sternberg memory paradigm, with subjects memorizing groups of 1, 3, 5 and 7 letters. We have looked at imaging data of 1vFix, 3vFix, 5vFix, 7vFix, and then our regression analysis, in theory, we should see areas of significant linear pattern when moving from the activation between 1, 3, 5, and 7 letters. However, in our latest analyses, the regression maps have not been complimenting some of the individual subjects' 1,3,etc vs Fix data. In the attached PDF, there are 2 subjects with their 1vFix, 3vFix, etc maps shown, as well as the regression map in the middle, and as you can see, particularly for the 2nd subject, the regression map just doesn't make sense considering the maps from which it was derived. The third sheet of the excel file plots the ROI values generated from the regression analysis against a calculated slope derived from the funcroi values from 1, 3, 5, and 7 vs Fix. The two outliers in the top left are the subjects we further analyzed in the attached powerpoint (which includes ROI derived values). Another strange occurance is that when making regression maps for sub-groups of approx. 8 subjects, the maps don't seems to match up well with the numbers, but the regression map of all of our subjects together looks great, yet the average ROI derived value is quite low. We've been searching for a few days for a stupid mistake that could have caused this, but nothing is popping out. I'm attached the analysis info for the regression analysis as well as an example paradigm file for that analysis (slopepar). We just are not sure why the regression maps and individual subject ROI values are so low consider the rather strong regression effect implied from simply eyeballing the data. I understand that the maps may not always be as strong as anticipated, but they should certainly not show dark negative blue when the pattern is positive. Examples of group commands: isxconcat-sess -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/9_ActiveFolate_Post_5T -d /cluster/roffman/users/Stable5_PerRun -analysis SIRP_LoadRegression_Stable5 -c Cond2vFix -o /cluster/roffman/users/Stable5_PerRun/August_2011/9_ActiveFolate_Post_5T_TEST mri_glmfit --y /cluster/roffman/users/Stable5_PerRun/August_2011/9_ActiveFolate_Post_5T_TEST/SIRP_LoadRegression_Stable5/Cond2vFix/lh.ces.nii --fsgd /cluster/roffman/users/fsgd/9_ActiveFolate_Post_5T.fsgd --osgm --glmdir /cluster/roffman/users/Stable5_PerRun/August_2011/9_ActiveFolate_Post_5T_TEST/SIRP_LoadRegression_Stable5/osgm/LH2vFix --surf fsaverage lh --fwhm 4.6 Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital niten...@nmr.mgh.harvard.edu Phone: 617-643-3215 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Coordinate transformations from orig/001.mgz to T1.mgz
The matrix that converts col-row-slice in the conformed space to that of the raw space is V = inv(Sr)*Sc where Sr and Sc are the vox2ras matricies of the raw (ie, dicom) and conformed spaces. You can get this matrix using mri_info --vox2ras --vox2ras-tkr gives the vox2ras in the tkregister space of the input. This is a slightly non-sensical space that is unique to FS (see that PDF for more info). doug Aapo Nummenmaa wrote: Yeah, that should be enough. Basically it is just a coordinate shift, then? I can (probably) figure out remaining part of the transformation to the TMS system. By the way, when I use mri_info --vox2ras-tkr on the original data (which is PIL), does it give me the vox2ras on the conformed (LIA) or the original (PIL) coordinate system? I would guess the conformed? Thanks, -Aapo On Aug 22, 2011, at 2:06 PM, Douglas N Greve wrote: Do you just need a vox2vox that goes from the conformed space back to the original dicom space? That's pretty easy, if that's the case. doug Aapo Nummenmaa wrote: Hi Doug, thanks for the reply. I have looked at the document and know approximately how things are defined. Our target TMS coordinate system is defined in terms of the original DICOM data and is LSA, independent of how the data was acquired (let's say it is PIL). I know naturally how to go from PIL to RAS to LSA and so forth within this volume. I operate with MATLAB, so when I load this stuff in, I can see if the column-row-slice order actually is LIA, PIL or whatnot mri_info says. But once the original data is processed by FS, to my understanding the data is conformed to be isotropic 1 mm voxels with matrix 256x256x256 and orientation LIA. So Tommi's question is can we incorporate this resampling procedure to obtain some kind of voxel-to-voxel transformation directly. It should be straightforward in principle, but I'm not sure what FreeSurfer exactly does during this resampling step. Assuming isotropic 1mm voxels to begin with, it seems to zero-fill the volume keeping the center of the FOV fixed. For now, I have just reverse engineered the voxel to voxel (or rather XYZ to XYZ) transformation by identifying same anatomical landmarks in the TMS and FreeSurfer coordinates. I guess we can also use bbregister to co-register the original data with orig.mgz (or T1.mgz) as an /ad hoc /solution. But of course, as Tommi pointed out, if the transformation can be figured out directly, that would be the nicest option. Thanks, -Aapo On Aug 22, 2011, at 11:55 AM, Douglas N Greve wrote: Hi Tommi, have you looked at this document? http://www.freesurfer.net/fswiki/CoordinateSystems?action=AttachFiledo=gettarget=fscoordinates.pdf http://www.freesurfer.net/fswiki/CoordinateSystems?action=AttachFiledo=gettarget=fscoordinates.pdf doug r...@nmr.mgh.harvard.edu wrote: Hi, We (Aapo Nummenmaa and I) are developing cross-platform software that would allow translating third-party coordinates back and forth with Freesurfer segmentations. Our example structural image is MEMPRAGE_4e_p2_1mm_iso (1 mm isotropic, 192 sagittal slices, T1 weighting). Our third-party system (TMS-navigator Nexstim NBS) uses DICOM/nifti with origin (0,0,0) at right posterior inferior corner of the stack with x=R-L y=I-S z=P-A. Our goal is to relate the Nexstim NBS coordinates to these two images: 1. $SUBJECTS_DIR/$SUBJECT/mri/orig/001.mgz (not altered by recon-all) 2. $SUBJECTS_DIR/$SUBJECT/mri/T1.mgz (altered by recon-all) For (1) above, Volume Index in tkmedit looks like this: origin (0,0,0) is at right anterior superior corner of the stack with x=A-P y=S-I z=R-L. Max values in tkmedit display were (255,243,191). The acquisition had 192 sagittal slices so the last number makes sense - not sure why the second figure is not 255 (perhaps just a display thing). The orig/001.mgz stack should be exactly the same stack as in the Nexstim NBS image (which is just the plain DICOM), without any resampling or other processing, just the axes have been reshuffled a bit. For (2) above, Volume Index in tkmedit looks like this: origin (0,0,0) is at right posterior superior corner of the stack with x=R-L y=S-I z=P-A. Max values in tkmedit display were (255,255,255). This makes things difficult, as we do not know what exactly recon-all did to orig/001.mgz when it converted it into T1.mgz. Our question is this: Is there a deterministic way to go from orig/001.mgz to T1.mgz Volume Index coordinates? It seems that recon-all has at least added sagittal slices to make the T1.mgz stack into a cube (looking at lateral shift between 001.mgz and T1.mgz, I would guess that 32 1-mm slices on both sides (2*32+192=256) were added)... Further, it is not clear if the orig/001.mgz volume has been shifted, rotated, or resampled by recon-all when turning it into T1.mgz. Thank you for the advice! Bests, Tommi Aapo
[Freesurfer] cortical thickness in freesurfer 3.02 vs 4.5
Hi, We are concerned about differences of cortical thickness when we process the same scans in freesurfer 4.5 and 3.02. We have attached an excel spreadsheet of the differences in thickness between 4.5 and 3.02 using the mean thickness of parcellations of both versions in both hemispheres. The difference in the paracellations vary from 3-11% between the versions. Are these findings reliable and explainable in choosing freesurfer 4.5 as our final version. Any comment are greatly appreciated, Thanks! Rune ___ 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] Coordinate transformations from orig/001.mgz to T1.mgz
Doug, thanks for the help, just to make sure: Does the ras in the raw data voxel2ras refer to the same RAS as in the conformed volume: The reason why I ask is that for the conformed volume, the voxel2ras direction cosines consist of -1,0, 1, whereas in the original this is not (exactly) the case. If the whole vox2ras transformation would be just flipping the orthogonal axes plus translation, then we should expect only -1,0, 1. for the values of the direction cosines for both vox2ras matrices, right? --ORIGINAL RAW VOXEL TO RAS-- 0.0587 -0.0437 -0.997393.2015 -0.9982 0.0128 -0.0593 161.2992 -0.0153 -0.9990 0.0429 112.8152 0. 0. 0. 1. --CONFORMED VOXEL TO RAS-- -1. -0. -0. 135.3584 0. -0. 1. -98.0502 0. -1. -0. 114.7583 0. 0. 0. 1. Thanks, -Aapo On Aug 22, 2011, at 3:10 PM, Douglas N Greve wrote: The matrix that converts col-row-slice in the conformed space to that of the raw space is V = inv(Sr)*Sc where Sr and Sc are the vox2ras matricies of the raw (ie, dicom) and conformed spaces. You can get this matrix using mri_info --vox2ras --vox2ras-tkr gives the vox2ras in the tkregister space of the input. This is a slightly non-sensical space that is unique to FS (see that PDF for more info). doug Aapo Nummenmaa wrote: Yeah, that should be enough. Basically it is just a coordinate shift, then? I can (probably) figure out remaining part of the transformation to the TMS system. By the way, when I use mri_info --vox2ras-tkr on the original data (which is PIL), does it give me the vox2ras on the conformed (LIA) or the original (PIL) coordinate system? I would guess the conformed? Thanks, -Aapo On Aug 22, 2011, at 2:06 PM, Douglas N Greve wrote: Do you just need a vox2vox that goes from the conformed space back to the original dicom space? That's pretty easy, if that's the case. doug Aapo Nummenmaa wrote: Hi Doug, thanks for the reply. I have looked at the document and know approximately how things are defined. Our target TMS coordinate system is defined in terms of the original DICOM data and is LSA, independent of how the data was acquired (let's say it is PIL). I know naturally how to go from PIL to RAS to LSA and so forth within this volume. I operate with MATLAB, so when I load this stuff in, I can see if the column-row-slice order actually is LIA, PIL or whatnot mri_info says. But once the original data is processed by FS, to my understanding the data is conformed to be isotropic 1 mm voxels with matrix 256x256x256 and orientation LIA. So Tommi's question is can we incorporate this resampling procedure to obtain some kind of voxel-to-voxel transformation directly. It should be straightforward in principle, but I'm not sure what FreeSurfer exactly does during this resampling step. Assuming isotropic 1mm voxels to begin with, it seems to zero-fill the volume keeping the center of the FOV fixed. For now, I have just reverse engineered the voxel to voxel (or rather XYZ to XYZ) transformation by identifying same anatomical landmarks in the TMS and FreeSurfer coordinates. I guess we can also use bbregister to co-register the original data with orig.mgz (or T1.mgz) as an /ad hoc /solution. But of course, as Tommi pointed out, if the transformation can be figured out directly, that would be the nicest option. Thanks, -Aapo On Aug 22, 2011, at 11:55 AM, Douglas N Greve wrote: Hi Tommi, have you looked at this document? http://www.freesurfer.net/fswiki/CoordinateSystems?action=AttachFiledo=gettarget=fscoordinates.pdf http://www.freesurfer.net/fswiki/CoordinateSystems?action=AttachFiledo=gettarget=fscoordinates.pdf doug r...@nmr.mgh.harvard.edu wrote: Hi, We (Aapo Nummenmaa and I) are developing cross-platform software that would allow translating third-party coordinates back and forth with Freesurfer segmentations. Our example structural image is MEMPRAGE_4e_p2_1mm_iso (1 mm isotropic, 192 sagittal slices, T1 weighting). Our third-party system (TMS-navigator Nexstim NBS) uses DICOM/nifti with origin (0,0,0) at right posterior inferior corner of the stack with x=R-L y=I-S z=P-A. Our goal is to relate the Nexstim NBS coordinates to these two images: 1. $SUBJECTS_DIR/$SUBJECT/mri/orig/001.mgz (not altered by recon-all) 2. $SUBJECTS_DIR/$SUBJECT/mri/T1.mgz (altered by recon-all) For (1) above, Volume Index in tkmedit looks like this: origin (0,0,0) is at right anterior superior corner of the stack with x=A-P y=S-I z=R-L. Max values in tkmedit display were (255,243,191). The acquisition
Re: [Freesurfer] Coordinate transformations from orig/001.mgz to T1.mgz
If you used mri_convert to convert from dicom to mgz, then the RAS in the vox2ras will be scanner coordinates for both the raw and conformed. During the conforming step, the volume is re-sliced to be aligned with the RAS coords, so the direction cosines are always +1/-1/0 doug Aapo Nummenmaa wrote: Doug, thanks for the help, just to make sure: Does the ras in the raw data voxel2ras refer to the same RAS as in the conformed volume: The reason why I ask is that for the conformed volume, the voxel2ras direction cosines consist of -1,0, 1, whereas in the original this is not (exactly) the case. If the whole vox2ras transformation would be just flipping the orthogonal axes plus translation, then we should expect only -1,0, 1. for the values of the direction cosines for both vox2ras matrices, right? --ORIGINAL RAW VOXEL TO RAS-- 0.0587 -0.0437 -0.997393.2015 -0.9982 0.0128 -0.0593 161.2992 -0.0153 -0.9990 0.0429 112.8152 0. 0. 0. 1. --CONFORMED VOXEL TO RAS-- -1. -0. -0. 135.3584 0. -0. 1. -98.0502 0. -1. -0. 114.7583 0. 0. 0. 1. Thanks, -Aapo On Aug 22, 2011, at 3:10 PM, Douglas N Greve wrote: The matrix that converts col-row-slice in the conformed space to that of the raw space is V = inv(Sr)*Sc where Sr and Sc are the vox2ras matricies of the raw (ie, dicom) and conformed spaces. You can get this matrix using mri_info --vox2ras --vox2ras-tkr gives the vox2ras in the tkregister space of the input. This is a slightly non-sensical space that is unique to FS (see that PDF for more info). doug Aapo Nummenmaa wrote: Yeah, that should be enough. Basically it is just a coordinate shift, then? I can (probably) figure out remaining part of the transformation to the TMS system. By the way, when I use mri_info --vox2ras-tkr on the original data (which is PIL), does it give me the vox2ras on the conformed (LIA) or the original (PIL) coordinate system? I would guess the conformed? Thanks, -Aapo On Aug 22, 2011, at 2:06 PM, Douglas N Greve wrote: Do you just need a vox2vox that goes from the conformed space back to the original dicom space? That's pretty easy, if that's the case. doug Aapo Nummenmaa wrote: Hi Doug, thanks for the reply. I have looked at the document and know approximately how things are defined. Our target TMS coordinate system is defined in terms of the original DICOM data and is LSA, independent of how the data was acquired (let's say it is PIL). I know naturally how to go from PIL to RAS to LSA and so forth within this volume. I operate with MATLAB, so when I load this stuff in, I can see if the column-row-slice order actually is LIA, PIL or whatnot mri_info says. But once the original data is processed by FS, to my understanding the data is conformed to be isotropic 1 mm voxels with matrix 256x256x256 and orientation LIA. So Tommi's question is can we incorporate this resampling procedure to obtain some kind of voxel-to-voxel transformation directly. It should be straightforward in principle, but I'm not sure what FreeSurfer exactly does during this resampling step. Assuming isotropic 1mm voxels to begin with, it seems to zero-fill the volume keeping the center of the FOV fixed. For now, I have just reverse engineered the voxel to voxel (or rather XYZ to XYZ) transformation by identifying same anatomical landmarks in the TMS and FreeSurfer coordinates. I guess we can also use bbregister to co-register the original data with orig.mgz (or T1.mgz) as an /ad hoc /solution. But of course, as Tommi pointed out, if the transformation can be figured out directly, that would be the nicest option. Thanks, -Aapo On Aug 22, 2011, at 11:55 AM, Douglas N Greve wrote: Hi Tommi, have you looked at this document? http://www.freesurfer.net/fswiki/CoordinateSystems?action=AttachFiledo=gettarget=fscoordinates.pdf http://www.freesurfer.net/fswiki/CoordinateSystems?action=AttachFiledo=gettarget=fscoordinates.pdf doug r...@nmr.mgh.harvard.edu wrote: Hi, We (Aapo Nummenmaa and I) are developing cross-platform software that would allow translating third-party coordinates back and forth with Freesurfer segmentations. Our example structural image is MEMPRAGE_4e_p2_1mm_iso (1 mm isotropic, 192 sagittal slices, T1 weighting). Our third-party system (TMS-navigator Nexstim NBS) uses DICOM/nifti with origin (0,0,0) at right posterior inferior corner of the stack with x=R-L y=I-S z=P-A. Our goal is to relate the Nexstim NBS coordinates to these two
[Freesurfer] the Subcortical Segmentation and the Cortical Parcellation
Hello All, I have a question about segmentation and parcellation. What is the difference between the subcortical segmentation and the cortical parcellation? Especially I do not understand the difference between subcortical and cortical and between segmentation and parcellation. I tried to read FreeSurfer Wiki, but I did not understand it well. Could you tell me it? Thanks. Kenichiro Tanaka. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] the Subcortical Segmentation and the Cortical Parcellation
The subcortical segmentation identifies subcortical structures such as thalamus, basal ganglia structures, hippocampus, amygdala, and cerebellum. The cortical parcellation delineates different areas of the cortex, such as the superior temporal sulcus, the central sulcus, the pars triangularis, opercularis, and orbitalis of the inferior frontal gyrus. A recommendation is to get a copy of the Duvernoy atlas, which covers definitions of different parts of the cortex. The Mai atlas is good for learning subcortical structures. On 8/22/11 9:45 PM, Kenichiro Tanaka wrote: Hello All, I have a question about segmentation and parcellation. What is the difference between the subcortical segmentation and the cortical parcellation? Especially I do not understand the difference between subcortical and cortical and between segmentation and parcellation. I tried to read FreeSurfer Wiki, but I did not understand it well. Could you tell me it? Thanks. Kenichiro Tanaka. ___ 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. -- Anthony Steven Dick, Ph.D. Assistant Professor Department of Psychology Florida International University Modesto A. Maidique Campus DM 296B 11200 S.W. 8th Street Miami, FL 33199 Phone: 305-348-4202 Fax: 305-348-3879 Email: ad...@fiu.edu Webpage: http://www.fiu.edu/~adick ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
