Re: [Freesurfer] Tracula the inverse of TBSS results
Fantastic! I love problems that solve themselves :) I won't be at ISMRM, but I'd be interested in seeing your results. On Sun, 7 Apr 2013, Sean Hatton wrote: I reinitialised the tracts and they all make sense now :) Hope to see you all at ISMRM. Sean Hatton Brain and Mind Research Institute University of Sydney. On 5/04/13 7:21 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: It's the pathstats.byvoxel.txt file. On Thu, 4 Apr 2013, Sean Hatton wrote: There are no extreme outliers (only 3 moderate outliers). Regarding the position, is that the FA center measures? Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: The increase in FA in patients is strange indeed. Are there any outliers in the tract averages? (Sorry if you've already mentioned this.) There are definitely situations in which TBSS and tracula would give you different results, since tracula gives you average FA in a large bundle, whereas TBSS gives voxel-based differences, where the voxels are on the skeleton of the white matter. So you could imagine a situation where part of a tract shows a decrease and other parts don't. Have you looked at the FA as a function of position along the tract from tracula (the other stats file that it gives you)? On Thu, 4 Apr 2013, Sean Hatton wrote: Yes, TBSS has reductions in FA in the patients' ATR cf controls (TFCE corrected, p. 05), but extracting the path stats in Tracula have the patients' ATR FA increased cf controls (independent t test, p. 05, uncorrected as per Yendiki et al. 2011). Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hm, it doesn't sound like a failure in the tract reconstruction then. What areas does TBSS give you differences in? Is it in the area of the same tracts? On Thu, 4 Apr 2013, Sean Hatton wrote: Hi Anastasia, An independent T-test on the aseg.stats WM-Hypointensties (SegId 77) showed that the mean WM hypointensities volume of the patient group (1378.8mm3, SD 650mm3) did not significantly differ from the controls (1120.8mm3, SD 372mm3; p=.111). A Pearson and Spearman correlation analysis found no correlation of WMH volume with tract volumes but did find a correlation with FA in three of the nine tracts of interest (Forceps minor, left ATR, left ILF). I reviewed the T2-FLAIRs for the subjects with the highest volumes of WM lesions and they were all dirty-appearing white matter around the ventricles rather than punctate WMH within the regions of these tracts. The tracts look reasonable in FreeviewŠ scratching head Sean On 4/04/13 7:17 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Sean - Can you check their freesurfer aseg's and see if any of the white matter was classified as a hypointensity there? a.y On Wed, 3 Apr 2013, Sean Hatton wrote: This is Tracula 5.2 with FLIRT and the vectors are correctly aligned (V1 over FA). From the literature and what is seen in my TBSS is reduced FA in the minor forceps and ATR. These are young (23yo) psychiatric so age related atrophy is not expected. However, they are known to have WM hypointensities even at a young age, I can review their T2s. A few are on mood stabilizers, but if this affected FA I would also see it in TBSS. Thoughts? Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Oh, another question: do your patients have white-mater hypo/hyper-intensities, in other words any voxels in the white matter that are classified as something other than white matter in the freesurfer aseg? On Wed, 3 Apr 2013, Sean Hatton wrote: Hi Freesurfer gurus, I have been using Tracula to investigate white matter abnormalities in a patient cohort (n=20) compared to matched controls (n=40). In line with the literature, we expected to see reductions in FA in the patients' tracts but instead they have significantly higher FA means. To double-check, we ran TBSS over the same cohorts and got the results as per the literature (I.e. reduced FA in the patient group). The FA, RD, AD, MD and volume outputs are normally distributed and there are no extreme outliners. So wondering: 1. The patient group had significantly reduced tract volumes. If this volume calculation is incorrect I expect it could influence the calculation of the mean FA, RD, AD etc. Is there a way of checking the volume and subsequent calculations? 2. Yendiki et al 2011 had no corrections do I need corrections? 3. Should I be thresholding tract stats? Thank you in advance, Sean Hatton Brain and Mind Research Institute University of Sydney 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] Tracula the inverse of TBSS results
I reinitialised the tracts and they all make sense now :) Hope to see you all at ISMRM. Sean Hatton Brain and Mind Research Institute University of Sydney. On 5/04/13 7:21 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: It's the pathstats.byvoxel.txt file. On Thu, 4 Apr 2013, Sean Hatton wrote: There are no extreme outliers (only 3 moderate outliers). Regarding the position, is that the FA center measures? Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: The increase in FA in patients is strange indeed. Are there any outliers in the tract averages? (Sorry if you've already mentioned this.) There are definitely situations in which TBSS and tracula would give you different results, since tracula gives you average FA in a large bundle, whereas TBSS gives voxel-based differences, where the voxels are on the skeleton of the white matter. So you could imagine a situation where part of a tract shows a decrease and other parts don't. Have you looked at the FA as a function of position along the tract from tracula (the other stats file that it gives you)? On Thu, 4 Apr 2013, Sean Hatton wrote: Yes, TBSS has reductions in FA in the patients' ATR cf controls (TFCE corrected, p. 05), but extracting the path stats in Tracula have the patients' ATR FA increased cf controls (independent t test, p. 05, uncorrected as per Yendiki et al. 2011). Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hm, it doesn't sound like a failure in the tract reconstruction then. What areas does TBSS give you differences in? Is it in the area of the same tracts? On Thu, 4 Apr 2013, Sean Hatton wrote: Hi Anastasia, An independent T-test on the aseg.stats WM-Hypointensties (SegId 77) showed that the mean WM hypointensities volume of the patient group (1378.8mm3, SD 650mm3) did not significantly differ from the controls (1120.8mm3, SD 372mm3; p=.111). A Pearson and Spearman correlation analysis found no correlation of WMH volume with tract volumes but did find a correlation with FA in three of the nine tracts of interest (Forceps minor, left ATR, left ILF). I reviewed the T2-FLAIRs for the subjects with the highest volumes of WM lesions and they were all dirty-appearing white matter around the ventricles rather than punctate WMH within the regions of these tracts. The tracts look reasonable in FreeviewŠ scratching head Sean On 4/04/13 7:17 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Sean - Can you check their freesurfer aseg's and see if any of the white matter was classified as a hypointensity there? a.y On Wed, 3 Apr 2013, Sean Hatton wrote: This is Tracula 5.2 with FLIRT and the vectors are correctly aligned (V1 over FA). From the literature and what is seen in my TBSS is reduced FA in the minor forceps and ATR. These are young (23yo) psychiatric so age related atrophy is not expected. However, they are known to have WM hypointensities even at a young age, I can review their T2s. A few are on mood stabilizers, but if this affected FA I would also see it in TBSS. Thoughts? Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Oh, another question: do your patients have white-mater hypo/hyper-intensities, in other words any voxels in the white matter that are classified as something other than white matter in the freesurfer aseg? On Wed, 3 Apr 2013, Sean Hatton wrote: Hi Freesurfer gurus, I have been using Tracula to investigate white matter abnormalities in a patient cohort (n=20) compared to matched controls (n=40). In line with the literature, we expected to see reductions in FA in the patients' tracts but instead they have significantly higher FA means. To double-check, we ran TBSS over the same cohorts and got the results as per the literature (I.e. reduced FA in the patient group). The FA, RD, AD, MD and volume outputs are normally distributed and there are no extreme outliners. So wondering: 1. The patient group had significantly reduced tract volumes. If this volume calculation is incorrect I expect it could influence the calculation of the mean FA, RD, AD etc. Is there a way of checking the volume and subsequent calculations? 2. Yendiki et al 2011 had no corrections do I need corrections? 3. Should I be thresholding tract stats? Thank you in advance, Sean Hatton Brain and Mind Research Institute University of Sydney 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] Tracula the inverse of TBSS results
Hi Anastasia, An independent T-test on the aseg.stats WM-Hypointensties (SegId 77) showed that the mean WM hypointensities volume of the patient group (1378.8mm3, SD 650mm3) did not significantly differ from the controls (1120.8mm3, SD 372mm3; p=.111). A Pearson and Spearman correlation analysis found no correlation of WMH volume with tract volumes but did find a correlation with FA in three of the nine tracts of interest (Forceps minor, left ATR, left ILF). I reviewed the T2-FLAIRs for the subjects with the highest volumes of WM lesions and they were all dirty-appearing white matter around the ventricles rather than punctate WMH within the regions of these tracts. The tracts look reasonable in Freeview… scratching head Sean On 4/04/13 7:17 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edumailto:ayend...@nmr.mgh.harvard.edu wrote: Hi Sean - Can you check their freesurfer aseg's and see if any of the white matter was classified as a hypointensity there? a.y On Wed, 3 Apr 2013, Sean Hatton wrote: This is Tracula 5.2 with FLIRT and the vectors are correctly aligned (V1 over FA). From the literature and what is seen in my TBSS is reduced FA in the minor forceps and ATR. These are young (23yo) psychiatric so age related atrophy is not expected. However, they are known to have WM hypointensities even at a young age, I can review their T2s. A few are on mood stabilizers, but if this affected FA I would also see it in TBSS. Thoughts? Anastasia Yendiki ayend...@nmr.mgh.harvard.edumailto:ayend...@nmr.mgh.harvard.edu wrote: Oh, another question: do your patients have white-mater hypo/hyper-intensities, in other words any voxels in the white matter that are classified as something other than white matter in the freesurfer aseg? On Wed, 3 Apr 2013, Sean Hatton wrote: Hi Freesurfer gurus, I have been using Tracula to investigate white matter abnormalities in a patient cohort (n=20) compared to matched controls (n=40). In line with the literature, we expected to see reductions in FA in the patients' tracts but instead they have significantly higher FA means. To double-check, we ran TBSS over the same cohorts and got the results as per the literature (I.e. reduced FA in the patient group). The FA, RD, AD, MD and volume outputs are normally distributed and there are no extreme outliners. So wondering: 1. The patient group had significantly reduced tract volumes. If this volume calculation is incorrect I expect it could influence the calculation of the mean FA, RD, AD etc. Is there a way of checking the volume and subsequent calculations? 2. Yendiki et al 2011 had no corrections – do I need corrections? 3. Should I be thresholding tract stats? Thank you in advance, Sean Hatton Brain and Mind Research Institute University of Sydney 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] Tracula the inverse of TBSS results
Hm, it doesn't sound like a failure in the tract reconstruction then. What areas does TBSS give you differences in? Is it in the area of the same tracts? On Thu, 4 Apr 2013, Sean Hatton wrote: Hi Anastasia, An independent T-test on the aseg.stats WM-Hypointensties (SegId 77) showed that the mean WM hypointensities volume of the patient group (1378.8mm3, SD 650mm3) did not significantly differ from the controls (1120.8mm3, SD 372mm3; p=.111). A Pearson and Spearman correlation analysis found no correlation of WMH volume with tract volumes but did find a correlation with FA in three of the nine tracts of interest (Forceps minor, left ATR, left ILF). I reviewed the T2-FLAIRs for the subjects with the highest volumes of WM lesions and they were all dirty-appearing white matter around the ventricles rather than punctate WMH within the regions of these tracts. The tracts look reasonable in Freeview… scratching head Sean On 4/04/13 7:17 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Sean - Can you check their freesurfer aseg's and see if any of the white matter was classified as a hypointensity there? a.y On Wed, 3 Apr 2013, Sean Hatton wrote: This is Tracula 5.2 with FLIRT and the vectors are correctly aligned (V1 over FA). From the literature and what is seen in my TBSS is reduced FA in the minor forceps and ATR. These are young (23yo) psychiatric so age related atrophy is not expected. However, they are known to have WM hypointensities even at a young age, I can review their T2s. A few are on mood stabilizers, but if this affected FA I would also see it in TBSS. Thoughts? Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Oh, another question: do your patients have white-mater hypo/hyper-intensities, in other words any voxels in the white matter that are classified as something other than white matter in the freesurfer aseg? On Wed, 3 Apr 2013, Sean Hatton wrote: Hi Freesurfer gurus, I have been using Tracula to investigate white matter abnormalities in a patient cohort (n=20) compared to matched controls (n=40). In line with the literature, we expected to see reductions in FA in the patients' tracts but instead they have significantly higher FA means. To double-check, we ran TBSS over the same cohorts and got the results as per the literature (I.e. reduced FA in the patient group). The FA, RD, AD, MD and volume outputs are normally distributed and there are no extreme outliners. So wondering: 1. The patient group had significantly reduced tract volumes. If this volume calculation is incorrect I expect it could influence the calculation of the mean FA, RD, AD etc. Is there a way of checking the volume and subsequent calculations? 2. Yendiki et al 2011 had no corrections – do I need corrections? 3. Should I be thresholding tract stats? Thank you in advance, Sean Hatton Brain and Mind Research Institute University of Sydney 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] Tracula the inverse of TBSS results
The increase in FA in patients is strange indeed. Are there any outliers in the tract averages? (Sorry if you've already mentioned this.) There are definitely situations in which TBSS and tracula would give you different results, since tracula gives you average FA in a large bundle, whereas TBSS gives voxel-based differences, where the voxels are on the skeleton of the white matter. So you could imagine a situation where part of a tract shows a decrease and other parts don't. Have you looked at the FA as a function of position along the tract from tracula (the other stats file that it gives you)? On Thu, 4 Apr 2013, Sean Hatton wrote: Yes, TBSS has reductions in FA in the patients' ATR cf controls (TFCE corrected, p. 05), but extracting the path stats in Tracula have the patients' ATR FA increased cf controls (independent t test, p. 05, uncorrected as per Yendiki et al. 2011). Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hm, it doesn't sound like a failure in the tract reconstruction then. What areas does TBSS give you differences in? Is it in the area of the same tracts? On Thu, 4 Apr 2013, Sean Hatton wrote: Hi Anastasia, An independent T-test on the aseg.stats WM-Hypointensties (SegId 77) showed that the mean WM hypointensities volume of the patient group (1378.8mm3, SD 650mm3) did not significantly differ from the controls (1120.8mm3, SD 372mm3; p=.111). A Pearson and Spearman correlation analysis found no correlation of WMH volume with tract volumes but did find a correlation with FA in three of the nine tracts of interest (Forceps minor, left ATR, left ILF). I reviewed the T2-FLAIRs for the subjects with the highest volumes of WM lesions and they were all dirty-appearing white matter around the ventricles rather than punctate WMH within the regions of these tracts. The tracts look reasonable in Freeview… scratching head Sean On 4/04/13 7:17 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Sean - Can you check their freesurfer aseg's and see if any of the white matter was classified as a hypointensity there? a.y On Wed, 3 Apr 2013, Sean Hatton wrote: This is Tracula 5.2 with FLIRT and the vectors are correctly aligned (V1 over FA). From the literature and what is seen in my TBSS is reduced FA in the minor forceps and ATR. These are young (23yo) psychiatric so age related atrophy is not expected. However, they are known to have WM hypointensities even at a young age, I can review their T2s. A few are on mood stabilizers, but if this affected FA I would also see it in TBSS. Thoughts? Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Oh, another question: do your patients have white-mater hypo/hyper-intensities, in other words any voxels in the white matter that are classified as something other than white matter in the freesurfer aseg? On Wed, 3 Apr 2013, Sean Hatton wrote: Hi Freesurfer gurus, I have been using Tracula to investigate white matter abnormalities in a patient cohort (n=20) compared to matched controls (n=40). In line with the literature, we expected to see reductions in FA in the patients' tracts but instead they have significantly higher FA means. To double-check, we ran TBSS over the same cohorts and got the results as per the literature (I.e. reduced FA in the patient group). The FA, RD, AD, MD and volume outputs are normally distributed and there are no extreme outliners. So wondering: 1. The patient group had significantly reduced tract volumes. If this volume calculation is incorrect I expect it could influence the calculation of the mean FA, RD, AD etc. Is there a way of checking the volume and subsequent calculations? 2. Yendiki et al 2011 had no corrections – do I need corrections? 3. Should I be thresholding tract stats? Thank you in advance, Sean Hatton Brain and Mind Research Institute University of Sydney 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] Tracula the inverse of TBSS results
There are no extreme outliers (only 3 moderate outliers). Regarding the position, is that the FA center measures? Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: The increase in FA in patients is strange indeed. Are there any outliers in the tract averages? (Sorry if you've already mentioned this.) There are definitely situations in which TBSS and tracula would give you different results, since tracula gives you average FA in a large bundle, whereas TBSS gives voxel-based differences, where the voxels are on the skeleton of the white matter. So you could imagine a situation where part of a tract shows a decrease and other parts don't. Have you looked at the FA as a function of position along the tract from tracula (the other stats file that it gives you)? On Thu, 4 Apr 2013, Sean Hatton wrote: Yes, TBSS has reductions in FA in the patients' ATR cf controls (TFCE corrected, p. 05), but extracting the path stats in Tracula have the patients' ATR FA increased cf controls (independent t test, p. 05, uncorrected as per Yendiki et al. 2011). Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hm, it doesn't sound like a failure in the tract reconstruction then. What areas does TBSS give you differences in? Is it in the area of the same tracts? On Thu, 4 Apr 2013, Sean Hatton wrote: Hi Anastasia, An independent T-test on the aseg.stats WM-Hypointensties (SegId 77) showed that the mean WM hypointensities volume of the patient group (1378.8mm3, SD 650mm3) did not significantly differ from the controls (1120.8mm3, SD 372mm3; p=.111). A Pearson and Spearman correlation analysis found no correlation of WMH volume with tract volumes but did find a correlation with FA in three of the nine tracts of interest (Forceps minor, left ATR, left ILF). I reviewed the T2-FLAIRs for the subjects with the highest volumes of WM lesions and they were all dirty-appearing white matter around the ventricles rather than punctate WMH within the regions of these tracts. The tracts look reasonable in Freeview… scratching head Sean On 4/04/13 7:17 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Sean - Can you check their freesurfer aseg's and see if any of the white matter was classified as a hypointensity there? a.y On Wed, 3 Apr 2013, Sean Hatton wrote: This is Tracula 5.2 with FLIRT and the vectors are correctly aligned (V1 over FA). From the literature and what is seen in my TBSS is reduced FA in the minor forceps and ATR. These are young (23yo) psychiatric so age related atrophy is not expected. However, they are known to have WM hypointensities even at a young age, I can review their T2s. A few are on mood stabilizers, but if this affected FA I would also see it in TBSS. Thoughts? Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Oh, another question: do your patients have white-mater hypo/hyper-intensities, in other words any voxels in the white matter that are classified as something other than white matter in the freesurfer aseg? On Wed, 3 Apr 2013, Sean Hatton wrote: Hi Freesurfer gurus, I have been using Tracula to investigate white matter abnormalities in a patient cohort (n=20) compared to matched controls (n=40). In line with the literature, we expected to see reductions in FA in the patients' tracts but instead they have significantly higher FA means. To double-check, we ran TBSS over the same cohorts and got the results as per the literature (I.e. reduced FA in the patient group). The FA, RD, AD, MD and volume outputs are normally distributed and there are no extreme outliners. So wondering: 1. The patient group had significantly reduced tract volumes. If this volume calculation is incorrect I expect it could influence the calculation of the mean FA, RD, AD etc. Is there a way of checking the volume and subsequent calculations? 2. Yendiki et al 2011 had no corrections – do I need corrections? 3. Should I be thresholding tract stats? Thank you in advance, Sean Hatton Brain and Mind Research Institute University of Sydney 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
Re: [Freesurfer] Tracula the inverse of TBSS results
It's the pathstats.byvoxel.txt file. On Thu, 4 Apr 2013, Sean Hatton wrote: There are no extreme outliers (only 3 moderate outliers). Regarding the position, is that the FA center measures? Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: The increase in FA in patients is strange indeed. Are there any outliers in the tract averages? (Sorry if you've already mentioned this.) There are definitely situations in which TBSS and tracula would give you different results, since tracula gives you average FA in a large bundle, whereas TBSS gives voxel-based differences, where the voxels are on the skeleton of the white matter. So you could imagine a situation where part of a tract shows a decrease and other parts don't. Have you looked at the FA as a function of position along the tract from tracula (the other stats file that it gives you)? On Thu, 4 Apr 2013, Sean Hatton wrote: Yes, TBSS has reductions in FA in the patients' ATR cf controls (TFCE corrected, p. 05), but extracting the path stats in Tracula have the patients' ATR FA increased cf controls (independent t test, p. 05, uncorrected as per Yendiki et al. 2011). Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hm, it doesn't sound like a failure in the tract reconstruction then. What areas does TBSS give you differences in? Is it in the area of the same tracts? On Thu, 4 Apr 2013, Sean Hatton wrote: Hi Anastasia, An independent T-test on the aseg.stats WM-Hypointensties (SegId 77) showed that the mean WM hypointensities volume of the patient group (1378.8mm3, SD 650mm3) did not significantly differ from the controls (1120.8mm3, SD 372mm3; p=.111). A Pearson and Spearman correlation analysis found no correlation of WMH volume with tract volumes but did find a correlation with FA in three of the nine tracts of interest (Forceps minor, left ATR, left ILF). I reviewed the T2-FLAIRs for the subjects with the highest volumes of WM lesions and they were all dirty-appearing white matter around the ventricles rather than punctate WMH within the regions of these tracts. The tracts look reasonable in Freeview… scratching head Sean On 4/04/13 7:17 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Sean - Can you check their freesurfer aseg's and see if any of the white matter was classified as a hypointensity there? a.y On Wed, 3 Apr 2013, Sean Hatton wrote: This is Tracula 5.2 with FLIRT and the vectors are correctly aligned (V1 over FA). From the literature and what is seen in my TBSS is reduced FA in the minor forceps and ATR. These are young (23yo) psychiatric so age related atrophy is not expected. However, they are known to have WM hypointensities even at a young age, I can review their T2s. A few are on mood stabilizers, but if this affected FA I would also see it in TBSS. Thoughts? Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Oh, another question: do your patients have white-mater hypo/hyper-intensities, in other words any voxels in the white matter that are classified as something other than white matter in the freesurfer aseg? On Wed, 3 Apr 2013, Sean Hatton wrote: Hi Freesurfer gurus, I have been using Tracula to investigate white matter abnormalities in a patient cohort (n=20) compared to matched controls (n=40). In line with the literature, we expected to see reductions in FA in the patients' tracts but instead they have significantly higher FA means. To double-check, we ran TBSS over the same cohorts and got the results as per the literature (I.e. reduced FA in the patient group). The FA, RD, AD, MD and volume outputs are normally distributed and there are no extreme outliners. So wondering: 1. The patient group had significantly reduced tract volumes. If this volume calculation is incorrect I expect it could influence the calculation of the mean FA, RD, AD etc. Is there a way of checking the volume and subsequent calculations? 2. Yendiki et al 2011 had no corrections – do I need corrections? 3. Should I be thresholding tract stats? Thank you in advance, Sean Hatton Brain and Mind Research Institute University of Sydney 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
Re: [Freesurfer] Tracula the inverse of TBSS results
Hi Sean - Are you using 5.1 or 5.2? What registration options are you using? Does your patient population have pronounced anatomical changes (e.g. atrophy) compared to controls? Which pathways did you expect to show reduced anisotropy in your patient population? Thanks, a.y On Wed, 3 Apr 2013, Sean Hatton wrote: Hi Freesurfer gurus, I have been using Tracula to investigate white matter abnormalities in a patient cohort (n=20) compared to matched controls (n=40). In line with the literature, we expected to see reductions in FA in the patients' tracts but instead they have significantly higher FA means. To double-check, we ran TBSS over the same cohorts and got the results as per the literature (I.e. reduced FA in the patient group). The FA, RD, AD, MD and volume outputs are normally distributed and there are no extreme outliners. So wondering: 1. The patient group had significantly reduced tract volumes. If this volume calculation is incorrect I expect it could influence the calculation of the mean FA, RD, AD etc. Is there a way of checking the volume and subsequent calculations? 2. Yendiki et al 2011 had no corrections – do I need corrections? 3. Should I be thresholding tract stats? Thank you in advance, Sean Hatton Brain and Mind Research Institute University of Sydney ___ 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] Tracula the inverse of TBSS results
Oh, another question: do your patients have white-mater hypo/hyper-intensities, in other words any voxels in the white matter that are classified as something other than white matter in the freesurfer aseg? On Wed, 3 Apr 2013, Sean Hatton wrote: Hi Freesurfer gurus, I have been using Tracula to investigate white matter abnormalities in a patient cohort (n=20) compared to matched controls (n=40). In line with the literature, we expected to see reductions in FA in the patients' tracts but instead they have significantly higher FA means. To double-check, we ran TBSS over the same cohorts and got the results as per the literature (I.e. reduced FA in the patient group). The FA, RD, AD, MD and volume outputs are normally distributed and there are no extreme outliners. So wondering: 1. The patient group had significantly reduced tract volumes. If this volume calculation is incorrect I expect it could influence the calculation of the mean FA, RD, AD etc. Is there a way of checking the volume and subsequent calculations? 2. Yendiki et al 2011 had no corrections – do I need corrections? 3. Should I be thresholding tract stats? Thank you in advance, Sean Hatton Brain and Mind Research Institute University of Sydney ___ 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.
