Re: [Freesurfer] Verifying ICV in FS5
Hi Jeff it looks pretty far off. Typically you want the surfaces to match the general shape of the brain cheers Bruce On Tue, 7 Feb 2012, Jeff Sadino wrote: Thank you Martin and Nick for the clarification about how to verify the talairach transformation in the newer FreeSurfers. I think I am going to use the -use-mritotal command, as this was giving more reasonable ICVs around 1.3L - 1.7L. I am still manually checking the outliers. According to the ICV measurement, this one seems way off, but I'm not sure how to judge the severity of the transform. On a scale of 1 to 10, 1 being bad, how would this one rate? How much would this cause the ICV to be off? Thank you, Jeff On Mon, Jan 30, 2012 at 8:47 AM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: Jeff, to check the tal reg, use: tkregister2 --s subjid --fstal --surfs i've corrected the eTIV page to reflect this. --fstal loads mni305 as the target. the target used in the tal reg step (711-2C...) is registered with the mni305. note that --surfs is optional, as the surfaces may not exist yet. Nick On Fri, 2012-01-27 at 18:53 -0500, Martin Reuter wrote: Hi Jeff, I am not sure about which atlas, but concerning the transforms: 4.2 and earlier: talairach_with_skull.lta later versions: talairach.xfm I am pretty convinced that the way to check as described here http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV cd $SUBJECTS_DIR/subject/mri/transforms tkregister2 --xfm talairach.xfm \ --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca \ --mov ../nu_noneck.mgz --reg junk is correct in newer FS versions, but maybe double check with Nick. Best, Martin On Fri, 2012-01-27 at 13:39 -1000, Jeff Sadino wrote: bump :) any feedback on this would be very much appreciated. Thank you! Jeff On Mon, Jan 23, 2012 at 6:56 PM, Jeff Sadino jsadino.que...@gmail.com wrote: Hello, Thank you Nick, Martin, and Doug for your previous feedback about ICV. I have a couple more questions that I am hoping you could clarify for me. To verify my ICV value, some pages on the mailing list and wiki say to use this command: tkregister2 --s subject --fstal --surf Other places say to use this: tkregister2 --xfm talairach.xfm --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca --mov ../nu_noneck.mgz --reg junk However, on this wiki page (http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV), it says that post fs4.2.0, the template is this file: 711-2C_as_mni_average_305.4dfp.img. In the first tkregister2 command above, doesn't the --fstal flag use the talairach template? But shouldn't it be using the 711 template? And since I am using fs5.0.0, does that mean that I should not be using the RB template? Ultimately, what is the correct way to verify the ICV in fs 5.0.0? Thank you very much, Jeff Sadino On Mon, Mar 1, 2010 at 7:57 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It's hard to tell from the coronal, but it looks ok. The problem is more visible in the sagittal. doug Jeff Sadino wrote: Hello Doug, I loaded up the tkregister2 program and I think I see some poor transformations. I've never really used it before though. Am I just looking at whether or not the green line lines up with the target image wm? Can you look at my pictures real quick? 040002_S04_test is from fs4 that is having problems. 040002_S04 is from fs3 and has a good icv value. Some of the blank spots are from my graphics drivers and unrelated to fs. tkregister2 also said the determinant of 040002_S04_test was 1.49544. Martin, Thank you for the idea. I did this, and got a much better icv. On fs3, where the icv was good, the number was 1,767,481. On fs4, it was 1,302,696. Using your idea on fs4, it was 1,819,485. Thank you so much to everyone for your help! Jeff On Thu, Feb 25, 2010 at 8:53 PM, Martin Kavec martin.ka...@gmail.com mailto:martin.ka...@gmail.com wrote: Hi Jeff, I see this relatively often. Eventhough the talairach registration is fine, the ICV is underestimated. In this case I take old ICV, which helps. mri_segstats --subject $MYSUBJECT --old-etiv-only This is in 99% of
Re: [Freesurfer] Verifying ICV in FS5
Jeff, to check the tal reg, use: tkregister2 --s subjid --fstal --surfs i've corrected the eTIV page to reflect this. --fstal loads mni305 as the target. the target used in the tal reg step (711-2C...) is registered with the mni305. note that --surfs is optional, as the surfaces may not exist yet. Nick On Fri, 2012-01-27 at 18:53 -0500, Martin Reuter wrote: Hi Jeff, I am not sure about which atlas, but concerning the transforms: 4.2 and earlier: talairach_with_skull.lta later versions: talairach.xfm I am pretty convinced that the way to check as described here http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV cd $SUBJECTS_DIR/subject/mri/transforms tkregister2 --xfm talairach.xfm \ --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca \ --mov ../nu_noneck.mgz --reg junk is correct in newer FS versions, but maybe double check with Nick. Best, Martin On Fri, 2012-01-27 at 13:39 -1000, Jeff Sadino wrote: bump :) any feedback on this would be very much appreciated. Thank you! Jeff On Mon, Jan 23, 2012 at 6:56 PM, Jeff Sadino jsadino.que...@gmail.com wrote: Hello, Thank you Nick, Martin, and Doug for your previous feedback about ICV. I have a couple more questions that I am hoping you could clarify for me. To verify my ICV value, some pages on the mailing list and wiki say to use this command: tkregister2 --s subject --fstal --surf Other places say to use this: tkregister2 --xfm talairach.xfm --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca --mov ../nu_noneck.mgz --reg junk However, on this wiki page (http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV), it says that post fs4.2.0, the template is this file: 711-2C_as_mni_average_305.4dfp.img. In the first tkregister2 command above, doesn't the --fstal flag use the talairach template? But shouldn't it be using the 711 template? And since I am using fs5.0.0, does that mean that I should not be using the RB template? Ultimately, what is the correct way to verify the ICV in fs 5.0.0? Thank you very much, Jeff Sadino On Mon, Mar 1, 2010 at 7:57 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It's hard to tell from the coronal, but it looks ok. The problem is more visible in the sagittal. doug Jeff Sadino wrote: Hello Doug, I loaded up the tkregister2 program and I think I see some poor transformations. I've never really used it before though. Am I just looking at whether or not the green line lines up with the target image wm? Can you look at my pictures real quick? 040002_S04_test is from fs4 that is having problems. 040002_S04 is from fs3 and has a good icv value. Some of the blank spots are from my graphics drivers and unrelated to fs. tkregister2 also said the determinant of 040002_S04_test was 1.49544. Martin, Thank you for the idea. I did this, and got a much better icv. On fs3, where the icv was good, the number was 1,767,481. On fs4, it was 1,302,696. Using your idea on fs4, it was 1,819,485. Thank you so much to everyone for your help! Jeff On Thu, Feb 25, 2010 at 8:53 PM, Martin Kavec martin.ka...@gmail.com mailto:martin.ka...@gmail.com wrote: Hi Jeff, I see this relatively often. Eventhough the talairach registration is fine, the ICV is underestimated. In this case I take old ICV, which helps. mri_segstats --subject $MYSUBJECT --old-etiv-only This is in 99% of these cases a cure. This is not just a blind attempt. In these cases I then compare each ICV normalized aseg volume against an age matched group and only if the old-etiv-only ICV gives better estimates I use it. Cheers, Martin On Thursday 25 February 2010 23:05:10 Jeff Sadino wrote: Thanks Doug. That is very good news to hear! Maybe I spoke too soon about fixing the problem. I looked at 4 more subjects, and even though the icv value is unique, its magnitude seems wrong. Often times, it is smaller than the BrainSegVol, which doesn't make much sense and it is also low overall. # subjectname 090167_F01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1639959, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1639959.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1289194.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1299686, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1299686.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1105595.114652, mm^3 #
Re: [Freesurfer] Verifying ICV in FS5
bump :) any feedback on this would be very much appreciated. Thank you! Jeff On Mon, Jan 23, 2012 at 6:56 PM, Jeff Sadino jsadino.que...@gmail.com wrote: Hello, Thank you Nick, Martin, and Doug for your previous feedback about ICV. I have a couple more questions that I am hoping you could clarify for me. To verify my ICV value, some pages on the mailing list and wiki say to use this command: tkregister2 --s subject --fstal --surf Other places say to use this: tkregister2 --xfm talairach.xfm --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca --mov ../nu_noneck.mgz --reg junk However, on this wiki page (http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV), it says that post fs4.2.0, the template is this file: 711-2C_as_mni_average_305.4dfp.img. In the first tkregister2 command above, doesn't the --fstal flag use the talairach template? But shouldn't it be using the 711 template? And since I am using fs5.0.0, does that mean that I should not be using the RB template? Ultimately, what is the correct way to verify the ICV in fs 5.0.0? Thank you very much, Jeff Sadino On Mon, Mar 1, 2010 at 7:57 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It's hard to tell from the coronal, but it looks ok. The problem is more visible in the sagittal. doug Jeff Sadino wrote: Hello Doug, I loaded up the tkregister2 program and I think I see some poor transformations. I've never really used it before though. Am I just looking at whether or not the green line lines up with the target image wm? Can you look at my pictures real quick? 040002_S04_test is from fs4 that is having problems. 040002_S04 is from fs3 and has a good icv value. Some of the blank spots are from my graphics drivers and unrelated to fs. tkregister2 also said the determinant of 040002_S04_test was 1.49544. Martin, Thank you for the idea. I did this, and got a much better icv. On fs3, where the icv was good, the number was 1,767,481. On fs4, it was 1,302,696. Using your idea on fs4, it was 1,819,485. Thank you so much to everyone for your help! Jeff On Thu, Feb 25, 2010 at 8:53 PM, Martin Kavec martin.ka...@gmail.com mailto:martin.ka...@gmail.com wrote: Hi Jeff, I see this relatively often. Eventhough the talairach registration is fine, the ICV is underestimated. In this case I take old ICV, which helps. mri_segstats --subject $MYSUBJECT --old-etiv-only This is in 99% of these cases a cure. This is not just a blind attempt. In these cases I then compare each ICV normalized aseg volume against an age matched group and only if the old-etiv-only ICV gives better estimates I use it. Cheers, Martin On Thursday 25 February 2010 23:05:10 Jeff Sadino wrote: Thanks Doug. That is very good news to hear! Maybe I spoke too soon about fixing the problem. I looked at 4 more subjects, and even though the icv value is unique, its magnitude seems wrong. Often times, it is smaller than the BrainSegVol, which doesn't make much sense and it is also low overall. # subjectname 090167_F01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1639959, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1639959.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1289194.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1299686, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1299686.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1105595.114652, mm^3 # subjectname 090182_S01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1599981, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1599981.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1199694.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1205382, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1205382.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1114008.197334, mm^3 # subjectname 090187_F01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1826694, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1826694.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1381871.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1388801, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1388801.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume,
Re: [Freesurfer] Verifying ICV in FS5
Hi Jeff, I am not sure about which atlas, but concerning the transforms: 4.2 and earlier: talairach_with_skull.lta later versions: talairach.xfm I am pretty convinced that the way to check as described here http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV cd $SUBJECTS_DIR/subject/mri/transforms tkregister2 --xfm talairach.xfm \ --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca \ --mov ../nu_noneck.mgz --reg junk is correct in newer FS versions, but maybe double check with Nick. Best, Martin On Fri, 2012-01-27 at 13:39 -1000, Jeff Sadino wrote: bump :) any feedback on this would be very much appreciated. Thank you! Jeff On Mon, Jan 23, 2012 at 6:56 PM, Jeff Sadino jsadino.que...@gmail.com wrote: Hello, Thank you Nick, Martin, and Doug for your previous feedback about ICV. I have a couple more questions that I am hoping you could clarify for me. To verify my ICV value, some pages on the mailing list and wiki say to use this command: tkregister2 --s subject --fstal --surf Other places say to use this: tkregister2 --xfm talairach.xfm --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca --mov ../nu_noneck.mgz --reg junk However, on this wiki page (http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV), it says that post fs4.2.0, the template is this file: 711-2C_as_mni_average_305.4dfp.img. In the first tkregister2 command above, doesn't the --fstal flag use the talairach template? But shouldn't it be using the 711 template? And since I am using fs5.0.0, does that mean that I should not be using the RB template? Ultimately, what is the correct way to verify the ICV in fs 5.0.0? Thank you very much, Jeff Sadino On Mon, Mar 1, 2010 at 7:57 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It's hard to tell from the coronal, but it looks ok. The problem is more visible in the sagittal. doug Jeff Sadino wrote: Hello Doug, I loaded up the tkregister2 program and I think I see some poor transformations. I've never really used it before though. Am I just looking at whether or not the green line lines up with the target image wm? Can you look at my pictures real quick? 040002_S04_test is from fs4 that is having problems. 040002_S04 is from fs3 and has a good icv value. Some of the blank spots are from my graphics drivers and unrelated to fs. tkregister2 also said the determinant of 040002_S04_test was 1.49544. Martin, Thank you for the idea. I did this, and got a much better icv. On fs3, where the icv was good, the number was 1,767,481. On fs4, it was 1,302,696. Using your idea on fs4, it was 1,819,485. Thank you so much to everyone for your help! Jeff On Thu, Feb 25, 2010 at 8:53 PM, Martin Kavec martin.ka...@gmail.com mailto:martin.ka...@gmail.com wrote: Hi Jeff, I see this relatively often. Eventhough the talairach registration is fine, the ICV is underestimated. In this case I take old ICV, which helps. mri_segstats --subject $MYSUBJECT --old-etiv-only This is in 99% of these cases a cure. This is not just a blind attempt. In these cases I then compare each ICV normalized aseg volume against an age matched group and only if the old-etiv-only ICV gives better estimates I use it. Cheers, Martin On Thursday 25 February 2010 23:05:10 Jeff Sadino wrote: Thanks Doug. That is very good news to hear! Maybe I spoke too soon about fixing the problem. I looked at 4 more subjects, and even though the icv value is unique, its magnitude seems wrong. Often times, it is smaller than the BrainSegVol, which doesn't make much sense and it is also low overall. # subjectname 090167_F01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1639959, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1639959.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1289194.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1299686, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1299686.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1105595.114652, mm^3 # subjectname 090182_S01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1599981, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1599981.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1199694.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1205382, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume,
[Freesurfer] Verifying ICV in FS5
Hello, Thank you Nick, Martin, and Doug for your previous feedback about ICV. I have a couple more questions that I am hoping you could clarify for me. To verify my ICV value, some pages on the mailing list and wiki say to use this command: tkregister2 --s subject --fstal --surf Other places say to use this: tkregister2 --xfm talairach.xfm --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca --mov ../nu_noneck.mgz --reg junk However, on this wiki page (http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV), it says that post fs4.2.0, the template is this file: 711-2C_as_mni_average_305.4dfp.img. In the first tkregister2 command above, doesn't the --fstal flag use the talairach template? But shouldn't it be using the 711 template? And since I am using fs5.0.0, does that mean that I should not be using the RB template? Ultimately, what is the correct way to verify the ICV in fs 5.0.0? Thank you very much, Jeff Sadino On Mon, Mar 1, 2010 at 7:57 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It's hard to tell from the coronal, but it looks ok. The problem is more visible in the sagittal. doug Jeff Sadino wrote: Hello Doug, I loaded up the tkregister2 program and I think I see some poor transformations. I've never really used it before though. Am I just looking at whether or not the green line lines up with the target image wm? Can you look at my pictures real quick? 040002_S04_test is from fs4 that is having problems. 040002_S04 is from fs3 and has a good icv value. Some of the blank spots are from my graphics drivers and unrelated to fs. tkregister2 also said the determinant of 040002_S04_test was 1.49544. Martin, Thank you for the idea. I did this, and got a much better icv. On fs3, where the icv was good, the number was 1,767,481. On fs4, it was 1,302,696. Using your idea on fs4, it was 1,819,485. Thank you so much to everyone for your help! Jeff On Thu, Feb 25, 2010 at 8:53 PM, Martin Kavec martin.ka...@gmail.com mailto:martin.ka...@gmail.com wrote: Hi Jeff, I see this relatively often. Eventhough the talairach registration is fine, the ICV is underestimated. In this case I take old ICV, which helps. mri_segstats --subject $MYSUBJECT --old-etiv-only This is in 99% of these cases a cure. This is not just a blind attempt. In these cases I then compare each ICV normalized aseg volume against an age matched group and only if the old-etiv-only ICV gives better estimates I use it. Cheers, Martin On Thursday 25 February 2010 23:05:10 Jeff Sadino wrote: Thanks Doug. That is very good news to hear! Maybe I spoke too soon about fixing the problem. I looked at 4 more subjects, and even though the icv value is unique, its magnitude seems wrong. Often times, it is smaller than the BrainSegVol, which doesn't make much sense and it is also low overall. # subjectname 090167_F01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1639959, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1639959.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1289194.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1299686, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1299686.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1105595.114652, mm^3 # subjectname 090182_S01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1599981, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1599981.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1199694.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1205382, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1205382.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1114008.197334, mm^3 # subjectname 090187_F01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1826694, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1826694.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 1381871.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 1388801, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 1388801.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1307759.303915, mm^3 # subjectname 100014_F01 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1948121, unitless # Measure BrainMask,
