Re: [Freesurfer] Reviewer questions...

[Jerome Maller]

Dear FreeSurfer experts,

Thankyou so much for your prompt and comprehensive responses! They are
excellent and will definitely guide me in how to respond to the Reviewers
of my manuscript.

Kind regards,

Jerome


On 14 January 2017 at 01:03, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> Thanks for your good points, Antonin.
>
> More on the matter:
>
> When segmenting standard resolution (~ 1mm) T1 scans, the position of the
> internal boundaries between the hippocampal substructures largely relies on
> prior knowledge acquired from our ex vivo training data and summarized
> in our statistical atlas. Therefore, the volumes of subfields around
> these boundaries (especially internal subfields such as the GC-DG and
> molecular layer) must be interpreted with caution, and further validation
> with higher resolution data should be carried out to confirm the results.
>
>  Having said that:
>
> 1. The fimbria is visible in 1 mm T1 data. It is true that, being a thin
> structure, its volume might be affected by motion artifacts more than
> that of other structures (see our Neuroimage paper linked by Antonin).
>
> 2. The hippocampus / amygdala interface is given by the alveus, which is a
> very thin structure, yielding a very faint (but not invisible) boundary in
> 1mm data, particularly if the scan is affected by motion. For that reason,
> automated methods sometimes make mistakes in that area, but they mostly get
> it right, partly thanks to the prior knowledge encoded in atlases.
>
> 3. The tail relies on geometric criteria for the anterior / posterior
> cut-off, but does not attempt to infer any internal boundaries, so it is
> definitely reliable even when segmented from 1 mm scans.
>
> Jerome, for your specific case:
>
> - The tail should not be problematic, for reason 3 above.
> - Schoemaker’s article, in addition to using an ancient version
> of FreeSurfer,  is about segmentation of infant MRI, which is more
> difficult that segmenting adults.
> - Volumetric protocol: see Table 2 of our Neuroimage paper describing the
> hippocampal atlas. For the tail: “we identified the first coronal
> slice (anterior to posterior) where the fornix is fully connected to the
> hippocampus, and labeled the whole hippocampus with this “umbrella” label
> in the remaining slices”.
> - The fimbria is visible (reason 1 above).
> - The molecular layer is not visible at 1 mm resolution, but you can still
> get and idea of its volume thanks to the prior - again, results based
> on such volumes should be interpreted with caution. However, if I
> understood correctly, your results are on the tail, and hence reliable
> (point 3).
>
> I hope this helps.
>
> Kind regards, and sorry for the long response!
>
> /Eugenio
>
> Juan Eugenio Iglesias
> ERC Senior Research Fellow
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
>
>
> On 13 Jan 2017, at 01:23, Antonin Skoch  wrote:
>
> Dear Jerome,
>
> I think I could chime in with my opinion: The Schoemaker et al paper
> results are based on hippocampus/amygdala segmentations in FreeSurfer 4.4.
>
> Hippocampal subfields segmentation module from development version you
> used should be more precise than 4.4. version and also the anatomical
> landmarks are well specified in paper Iglesias et al, 2015:
>
> https://www.ncbi.nlm.nih.gov/pubmed/25936807
> I think this paper can be used as a good basis for arguments to your
> reviewer.
>
> Concerning the reliability of estimation of particular hippocampal
> subfields, I think it also depend on what resolution was your input images,
> and whether you used additional high-resolution T2. The effect of various
> image resolution on the reliability of results is also well discussed in
> above-mentioned paper I think.
>
> Regards,
>
> Antonin Skoch
>
> ___
> 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.
>
>
>


-- 

*Dr Jerome J Maller   BSc,GradDipPsych,MSc,PhD*

Neuroscientist

Adjunct Senior Research Fellow

*Monash Alfred Psychiatry Research Centre (MAPrc)*

*Central Clinical School, Monash University and Alfred Hospital*

*4th Floor, 607 St Kilda Rd, Melbourne VIC*



Adjunct Associate Professor

*Centre for Research on Ageing, Health and Wellbeing, Research School of
Population Health, ANU College of Medicine, Biology and Environment at the
Australian National University.*



*T: +61 3 9076 2404*

*F: +61 3 9076 6588*

[Freesurfer] aparc stats file output

[Marianna Riello]

Dear Freesurfer users,

I have a question on the 'aparc.stats' file output:
Which of your label corresponds to:
Ventro and Dorso Lateral Prefrontal Cortex?
Supplementary motor areas?
Putamen?
Angular Gyrus?


Thank you for your help

Sincerely,
Marianna

___
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] surface based analysis (projfrac)

[Douglas N Greve]

Yes


On 01/13/2017 03:28 PM, John Anderson wrote:
> Thank you Doug for the advice ,
> I will follow your pipeline, I see that the command  "gtmseg " is part 
> of Freesurfer 6. Can I apply it on recons generated by Freesurfer 5.3 ?
> Best,
> John
> *Sent:* Friday, January 13, 2017 at 3:16 PM
> *From:* "Douglas N Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> These differences are hard to track down because they are so subtle.
>
> You may want to use our PET module, which includes PVC
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
>
>
> On 01/13/2017 03:10 PM, John Anderson wrote:
> > I am working on surface-based analysis to study the differnce in PET
> > signal in the cortex between two groups.
> > When I used "projfrac=0.5 " there was no differnce between the groups
> > at "cwp 0.05", and when I changed the "projfrac to 0" I got
> > significant differnce between the groups in specific areas at "cwp
> > 0.01". How can I check that this differnce is a real differnce and
> > not related to partial volume effect?
> > Best,
> > John
> > *Sent:* Friday, January 13, 2017 at 2:46 PM
> > *From:* "Douglas N Greve" 
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> > What is the modality you are looking at?
> >
> >
> > On 01/13/2017 02:08 PM, John Anderson wrote:
> > > Thank you very much Doug,
> > > Kindly, do you suggest me any steps to avoid patial volume effects in
> > > surface based analyses ?
> > > Best,
> > > John
> > > *Sent:* Friday, January 13, 2017 at 12:21 PM
> > > *From:* "Douglas N Greve" 
> > > *To:* freesurfer@nmr.mgh.harvard.edu
> > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> > >
> > >
> > > On 01/12/2017 05:20 PM, John Anderson wrote:
> > > > Thank you very much Doug and thank you for briniging the issue of
> > > > "partial volume effect " to my attention. Kindly, I have one last
> > > > question.
> > > > I found in wiki that the default values for projfrc value are 
> between
> > > > 0 and 1. Are there negative values? I mean for example "-2, -1, 
> 0 , 1,
> > > > 2 ", In other words, less than zero means the surface based analysis
> > > > is running at a lower level of the white matter.
> > > Yes
> > > > Can the issue of the partial volume effect be avoided by using 
> larger
> > > > numbers for "projfrac" ?
> > > No, PVEs can't be avoided that way.
> > > > Bests,
> > > > John
> > > > *Sent:* Thursday, January 12, 2017 at 5:08 PM
> > > > *From:* "Douglas N Greve" 
> > > > *To:* freesurfer@nmr.mgh.harvard.edu
> > > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> > > > yes, that is correct. However, understand that there might only be a
> > > > difference of 1mm between those two locations, so it could 
> easily be a
> > > > partial volume effect
> > > >
> > > >
> > > > On 01/11/2017 08:50 AM, John Anderson wrote:
> > > > > Thank you Doug,
> > > > > Exactly! I meant GM near the CC.
> > > > > When I used "projfrac=0.5 " there was no differnce between the
> > groups
> > > > > at "cwp 0.05", and when I changed the "projfrac to 0" I got
> > > > > significant differnce between the groups in specific areas at "cwp
> > > > > 0.01". Kindly, how can this be explained? I highly appreciate 
> if you
> > > > > help me to understand this point:
> > > > > For "projfrac =0" I expect the surface based analysis to
> > > > > be running close to white matter. Right? and when I used
> > > > > "projfrac=0.5" the analysis is running in the middle area
> > between pial
> > > > > and white. When the analysis is not showing any differne 
> between the
> > > > > groups for "projfrac 0.5" and showing differnce for "projfrac 0"
> > that
> > > > > means the differnce between the groups is deeper and closer to 
> white
> > > > > matter. Is this correct?
> > > > > Thank you for any input and clarification!
> > > > > Bests,
> > > > > John
> > > > > *Sent:* Tuesday, January 10, 2017 at 10:51 AM
> > > > > *From:* "Douglas Greve" 
> > > > > *To:* freesurfer@nmr.mgh.harvard.edu
> > > > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> > > > >
> > > > > When you say in the corpus callosum, do you mean in WM? The
> > > > > surface-based analysis is only for cortical GM. If you mean in
> > GM near
> > > > > the CC, then the analysis is appropriate. The projfrac parameter
> > sets
> > > > > the sampling location between the white and pial surfaces 
> where 0.5
> > > > > means half way.
> > > > >
> > > > > On 1/10/17 8:07 AM, John Anderson wrote:
> > > > >
> > > > > Dear FS experts,
> > > > > I am working on surface based analysis using freesurfer. I want to
> > > > > inquire about the flag "projfrac" in the command "mris_preproc"
> > > > > I ran voxel wise analysis including the same subjects. I found
> > > > > differnce between the groups in areas close to the corpus
> > > > > callosum. I want to get the same results using surface based
> > > > > a

Re: [Freesurfer] surface based analysis (projfrac)

[John Anderson]

Thank you Doug for the advice ,

I will follow your pipeline, I see that the command  "gtmseg " is part of Freesurfer 6. Can I apply it on recons generated by Freesurfer 5.3 ?
 

Best,
John




Sent: Friday, January 13, 2017 at 3:16 PM
From: "Douglas N Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis (projfrac)

These differences are hard to track down because they are so subtle.

You may want to use our PET module, which includes PVC

http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer


On 01/13/2017 03:10 PM, John Anderson wrote:
> I am working on surface-based analysis to study the differnce in PET
> signal in the cortex between two groups.
> When I used "projfrac=0.5 " there was no differnce between the groups
> at "cwp 0.05", and when I changed the "projfrac to 0" I got
> significant differnce between the groups in specific areas at "cwp
> 0.01". How can I check that this differnce is a real differnce and
> not related to partial volume effect?
> Best,
> John
> *Sent:* Friday, January 13, 2017 at 2:46 PM
> *From:* "Douglas N Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> What is the modality you are looking at?
>
>
> On 01/13/2017 02:08 PM, John Anderson wrote:
> > Thank you very much Doug,
> > Kindly, do you suggest me any steps to avoid patial volume effects in
> > surface based analyses ?
> > Best,
> > John
> > *Sent:* Friday, January 13, 2017 at 12:21 PM
> > *From:* "Douglas N Greve" 
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> >
> >
> > On 01/12/2017 05:20 PM, John Anderson wrote:
> > > Thank you very much Doug and thank you for briniging the issue of
> > > "partial volume effect " to my attention. Kindly, I have one last
> > > question.
> > > I found in wiki that the default values for projfrc value are between
> > > 0 and 1. Are there negative values? I mean for example "-2, -1, 0 , 1,
> > > 2 ", In other words, less than zero means the surface based analysis
> > > is running at a lower level of the white matter.
> > Yes
> > > Can the issue of the partial volume effect be avoided by using larger
> > > numbers for "projfrac" ?
> > No, PVEs can't be avoided that way.
> > > Bests,
> > > John
> > > *Sent:* Thursday, January 12, 2017 at 5:08 PM
> > > *From:* "Douglas N Greve" 
> > > *To:* freesurfer@nmr.mgh.harvard.edu
> > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> > > yes, that is correct. However, understand that there might only be a
> > > difference of 1mm between those two locations, so it could easily be a
> > > partial volume effect
> > >
> > >
> > > On 01/11/2017 08:50 AM, John Anderson wrote:
> > > > Thank you Doug,
> > > > Exactly! I meant GM near the CC.
> > > > When I used "projfrac=0.5 " there was no differnce between the
> groups
> > > > at "cwp 0.05", and when I changed the "projfrac to 0" I got
> > > > significant differnce between the groups in specific areas at "cwp
> > > > 0.01". Kindly, how can this be explained? I highly appreciate if you
> > > > help me to understand this point:
> > > > For "projfrac =0" I expect the surface based analysis to
> > > > be running close to white matter. Right? and when I used
> > > > "projfrac=0.5" the analysis is running in the middle area
> between pial
> > > > and white. When the analysis is not showing any differne between the
> > > > groups for "projfrac 0.5" and showing differnce for "projfrac 0"
> that
> > > > means the differnce between the groups is deeper and closer to white
> > > > matter. Is this correct?
> > > > Thank you for any input and clarification!
> > > > Bests,
> > > > John
> > > > *Sent:* Tuesday, January 10, 2017 at 10:51 AM
> > > > *From:* "Douglas Greve" 
> > > > *To:* freesurfer@nmr.mgh.harvard.edu
> > > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> > > >
> > > > When you say in the corpus callosum, do you mean in WM? The
> > > > surface-based analysis is only for cortical GM. If you mean in
> GM near
> > > > the CC, then the analysis is appropriate. The projfrac parameter
> sets
> > > > the sampling location between the white and pial surfaces where 0.5
> > > > means half way.
> > > >
> > > > On 1/10/17 8:07 AM, John Anderson wrote:
> > > >
> > > > Dear FS experts,
> > > > I am working on surface based analysis using freesurfer. I want to
> > > > inquire about the flag "projfrac" in the command "mris_preproc"
> > > > I ran voxel wise analysis including the same subjects. I found
> > > > differnce between the groups in areas close to the corpus
> > > > callosum. I want to get the same results using surface based
> > > > analysis. If I use the projfrac=0.5 is this able to show the same
> > > > results that I got in voxel wise analysis at the level of the
> > > > corpus callosum. Do I need to use differnt number for projfrac ?
> > > > Thank you for any advice.
> > > >
> > > > Best,
> > > > John
> > > >
> > > > 

Re: [Freesurfer] surface based analysis (projfrac)

[Douglas N Greve]

These differences are hard to track down because they are so subtle.

You may want to use our PET module, which includes PVC

http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer


On 01/13/2017 03:10 PM, John Anderson wrote:
> I am working on surface-based analysis to study the differnce in PET 
> signal in the cortex between two groups.
> When I used "projfrac=0.5 " there was no differnce between the groups 
> at "cwp 0.05", and when I changed the "projfrac to 0" I got 
> significant differnce between the groups in specific areas at "cwp 
> 0.01".  How can I check that this differnce is a real differnce and 
> not related to partial volume effect?
> Best,
> John
> *Sent:* Friday, January 13, 2017 at 2:46 PM
> *From:* "Douglas N Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> What is the modality you are looking at?
>
>
> On 01/13/2017 02:08 PM, John Anderson wrote:
> > Thank you very much Doug,
> > Kindly, do you suggest me any steps to avoid patial volume effects in
> > surface based analyses ?
> > Best,
> > John
> > *Sent:* Friday, January 13, 2017 at 12:21 PM
> > *From:* "Douglas N Greve" 
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> >
> >
> > On 01/12/2017 05:20 PM, John Anderson wrote:
> > > Thank you very much Doug and thank you for briniging the issue of
> > > "partial volume effect " to my attention. Kindly, I have one last
> > > question.
> > > I found in wiki that the default values for projfrc value are between
> > > 0 and 1. Are there negative values? I mean for example "-2, -1, 0 , 1,
> > > 2 ", In other words, less than zero means the surface based analysis
> > > is running at a lower level of the white matter.
> > Yes
> > > Can the issue of the partial volume effect be avoided by using larger
> > > numbers for "projfrac" ?
> > No, PVEs can't be avoided that way.
> > > Bests,
> > > John
> > > *Sent:* Thursday, January 12, 2017 at 5:08 PM
> > > *From:* "Douglas N Greve" 
> > > *To:* freesurfer@nmr.mgh.harvard.edu
> > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> > > yes, that is correct. However, understand that there might only be a
> > > difference of 1mm between those two locations, so it could easily be a
> > > partial volume effect
> > >
> > >
> > > On 01/11/2017 08:50 AM, John Anderson wrote:
> > > > Thank you Doug,
> > > > Exactly! I meant GM near the CC.
> > > > When I used "projfrac=0.5 " there was no differnce between the 
> groups
> > > > at "cwp 0.05", and when I changed the "projfrac to 0" I got
> > > > significant differnce between the groups in specific areas at "cwp
> > > > 0.01". Kindly, how can this be explained? I highly appreciate if you
> > > > help me to understand this point:
> > > > For "projfrac =0" I expect the surface based analysis to
> > > > be running close to white matter. Right? and when I used
> > > > "projfrac=0.5" the analysis is running in the middle area 
> between pial
> > > > and white. When the analysis is not showing any differne between the
> > > > groups for "projfrac 0.5" and showing differnce for "projfrac 0" 
> that
> > > > means the differnce between the groups is deeper and closer to white
> > > > matter. Is this correct?
> > > > Thank you for any input and clarification!
> > > > Bests,
> > > > John
> > > > *Sent:* Tuesday, January 10, 2017 at 10:51 AM
> > > > *From:* "Douglas Greve" 
> > > > *To:* freesurfer@nmr.mgh.harvard.edu
> > > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> > > >
> > > > When you say in the corpus callosum, do you mean in WM? The
> > > > surface-based analysis is only for cortical GM. If you mean in 
> GM near
> > > > the CC, then the analysis is appropriate. The projfrac parameter 
> sets
> > > > the sampling location between the white and pial surfaces where 0.5
> > > > means half way.
> > > >
> > > > On 1/10/17 8:07 AM, John Anderson wrote:
> > > >
> > > > Dear FS experts,
> > > > I am working on surface based analysis using freesurfer. I want to
> > > > inquire about the flag "projfrac" in the command "mris_preproc"
> > > > I ran voxel wise analysis including the same subjects. I found
> > > > differnce between the groups in areas close to the corpus
> > > > callosum. I want to get the same results using surface based
> > > > analysis. If I use the projfrac=0.5 is this able to show the same
> > > > results that I got in voxel wise analysis at the level of the
> > > > corpus callosum. Do I need to use differnt number for projfrac ?
> > > > Thank you for any advice.
> > > >
> > > > Best,
> > > > John
> > > >
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > >
> > > >
> > > > ___ Freesurfer mailing
> > > > list Freesurfer@nmr.mgh.harvard.edu
> > > > https://mail.nm

Re: [Freesurfer] surface based analysis (projfrac)

[John Anderson]

I am working on surface-based analysis to study the differnce in PET signal in the cortex between two groups.

When I used "projfrac=0.5 " there was no differnce between the groups at "cwp 0.05", and when I changed the "projfrac to 0" I got significant differnce between the groups in specific areas at "cwp 0.01".  How can I check that this differnce is a real differnce and not related to partial volume effect?

Best,
John 


 

Sent: Friday, January 13, 2017 at 2:46 PM
From: "Douglas N Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis (projfrac)

What is the modality you are looking at?


On 01/13/2017 02:08 PM, John Anderson wrote:
> Thank you very much Doug,
> Kindly, do you suggest me any steps to avoid patial volume effects in
> surface based analyses ?
> Best,
> John
> *Sent:* Friday, January 13, 2017 at 12:21 PM
> *From:* "Douglas N Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
>
>
> On 01/12/2017 05:20 PM, John Anderson wrote:
> > Thank you very much Doug and thank you for briniging the issue of
> > "partial volume effect " to my attention. Kindly, I have one last
> > question.
> > I found in wiki that the default values for projfrc value are between
> > 0 and 1. Are there negative values? I mean for example "-2, -1, 0 , 1,
> > 2 ", In other words, less than zero means the surface based analysis
> > is running at a lower level of the white matter.
> Yes
> > Can the issue of the partial volume effect be avoided by using larger
> > numbers for "projfrac" ?
> No, PVEs can't be avoided that way.
> > Bests,
> > John
> > *Sent:* Thursday, January 12, 2017 at 5:08 PM
> > *From:* "Douglas N Greve" 
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> > yes, that is correct. However, understand that there might only be a
> > difference of 1mm between those two locations, so it could easily be a
> > partial volume effect
> >
> >
> > On 01/11/2017 08:50 AM, John Anderson wrote:
> > > Thank you Doug,
> > > Exactly! I meant GM near the CC.
> > > When I used "projfrac=0.5 " there was no differnce between the groups
> > > at "cwp 0.05", and when I changed the "projfrac to 0" I got
> > > significant differnce between the groups in specific areas at "cwp
> > > 0.01". Kindly, how can this be explained? I highly appreciate if you
> > > help me to understand this point:
> > > For "projfrac =0" I expect the surface based analysis to
> > > be running close to white matter. Right? and when I used
> > > "projfrac=0.5" the analysis is running in the middle area between pial
> > > and white. When the analysis is not showing any differne between the
> > > groups for "projfrac 0.5" and showing differnce for "projfrac 0" that
> > > means the differnce between the groups is deeper and closer to white
> > > matter. Is this correct?
> > > Thank you for any input and clarification!
> > > Bests,
> > > John
> > > *Sent:* Tuesday, January 10, 2017 at 10:51 AM
> > > *From:* "Douglas Greve" 
> > > *To:* freesurfer@nmr.mgh.harvard.edu
> > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> > >
> > > When you say in the corpus callosum, do you mean in WM? The
> > > surface-based analysis is only for cortical GM. If you mean in GM near
> > > the CC, then the analysis is appropriate. The projfrac parameter sets
> > > the sampling location between the white and pial surfaces where 0.5
> > > means half way.
> > >
> > > On 1/10/17 8:07 AM, John Anderson wrote:
> > >
> > > Dear FS experts,
> > > I am working on surface based analysis using freesurfer. I want to
> > > inquire about the flag "projfrac" in the command "mris_preproc"
> > > I ran voxel wise analysis including the same subjects. I found
> > > differnce between the groups in areas close to the corpus
> > > callosum. I want to get the same results using surface based
> > > analysis. If I use the projfrac=0.5 is this able to show the same
> > > results that I got in voxel wise analysis at the level of the
> > > corpus callosum. Do I need to use differnt number for projfrac ?
> > > Thank you for any advice.
> > >
> > > Best,
> > > John
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> > > ___ 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 cont

Re: [Freesurfer] surface based analysis (projfrac)

[Douglas N Greve]

What is the modality you are looking at?


On 01/13/2017 02:08 PM, John Anderson wrote:
> Thank you very much Doug,
> Kindly, do you suggest me any steps to avoid patial volume effects in 
> surface based analyses ?
> Best,
> John
> *Sent:* Friday, January 13, 2017 at 12:21 PM
> *From:* "Douglas N Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
>
>
> On 01/12/2017 05:20 PM, John Anderson wrote:
> > Thank you very much Doug and thank you for briniging the issue of
> > "partial volume effect " to my attention. Kindly, I have one last
> > question.
> > I found in wiki that the default values for projfrc value are between
> > 0 and 1. Are there negative values? I mean for example "-2, -1, 0 , 1,
> > 2 ", In other words, less than zero means the surface based analysis
> > is running at a lower level of the white matter.
> Yes
> > Can the issue of the partial volume effect be avoided by using larger
> > numbers for "projfrac" ?
> No, PVEs can't be avoided that way.
> > Bests,
> > John
> > *Sent:* Thursday, January 12, 2017 at 5:08 PM
> > *From:* "Douglas N Greve" 
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> > yes, that is correct. However, understand that there might only be a
> > difference of 1mm between those two locations, so it could easily be a
> > partial volume effect
> >
> >
> > On 01/11/2017 08:50 AM, John Anderson wrote:
> > > Thank you Doug,
> > > Exactly! I meant GM near the CC.
> > > When I used "projfrac=0.5 " there was no differnce between the groups
> > > at "cwp 0.05", and when I changed the "projfrac to 0" I got
> > > significant differnce between the groups in specific areas at "cwp
> > > 0.01". Kindly, how can this be explained? I highly appreciate if you
> > > help me to understand this point:
> > > For "projfrac =0" I expect the surface based analysis to
> > > be running close to white matter. Right? and when I used
> > > "projfrac=0.5" the analysis is running in the middle area between pial
> > > and white. When the analysis is not showing any differne between the
> > > groups for "projfrac 0.5" and showing differnce for "projfrac 0" that
> > > means the differnce between the groups is deeper and closer to white
> > > matter. Is this correct?
> > > Thank you for any input and clarification!
> > > Bests,
> > > John
> > > *Sent:* Tuesday, January 10, 2017 at 10:51 AM
> > > *From:* "Douglas Greve" 
> > > *To:* freesurfer@nmr.mgh.harvard.edu
> > > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> > >
> > > When you say in the corpus callosum, do you mean in WM? The
> > > surface-based analysis is only for cortical GM. If you mean in GM near
> > > the CC, then the analysis is appropriate. The projfrac parameter sets
> > > the sampling location between the white and pial surfaces where 0.5
> > > means half way.
> > >
> > > On 1/10/17 8:07 AM, John Anderson wrote:
> > >
> > > Dear FS experts,
> > > I am working on surface based analysis using freesurfer. I want to
> > > inquire about the flag "projfrac" in the command "mris_preproc"
> > > I ran voxel wise analysis including the same subjects. I found
> > > differnce between the groups in areas close to the corpus
> > > callosum. I want to get the same results using surface based
> > > analysis. If I use the projfrac=0.5 is this able to show the same
> > > results that I got in voxel wise analysis at the level of the
> > > corpus callosum. Do I need to use differnt number for projfrac ?
> > > Thank you for any advice.
> > >
> > > Best,
> > > John
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> > > ___ 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
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
> 

Re: [Freesurfer] surface based analysis (projfrac)

[John Anderson]

Thank you very much Doug,

Kindly, do you suggest me any steps to avoid patial volume effects in surface based analyses ?
 

Best,
John 


 

Sent: Friday, January 13, 2017 at 12:21 PM
From: "Douglas N Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis (projfrac)



On 01/12/2017 05:20 PM, John Anderson wrote:
> Thank you very much Doug and thank you for briniging the issue of
> "partial volume effect " to my attention. Kindly, I have one last
> question.
> I found in wiki that the default values for projfrc value are between
> 0 and 1. Are there negative values? I mean for example "-2, -1, 0 , 1,
> 2 ", In other words, less than zero means the surface based analysis
> is running at a lower level of the white matter.
Yes
> Can the issue of the partial volume effect be avoided by using larger
> numbers for "projfrac" ?
No, PVEs can't be avoided that way.
> Bests,
> John
> *Sent:* Thursday, January 12, 2017 at 5:08 PM
> *From:* "Douglas N Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> yes, that is correct. However, understand that there might only be a
> difference of 1mm between those two locations, so it could easily be a
> partial volume effect
>
>
> On 01/11/2017 08:50 AM, John Anderson wrote:
> > Thank you Doug,
> > Exactly! I meant GM near the CC.
> > When I used "projfrac=0.5 " there was no differnce between the groups
> > at "cwp 0.05", and when I changed the "projfrac to 0" I got
> > significant differnce between the groups in specific areas at "cwp
> > 0.01". Kindly, how can this be explained? I highly appreciate if you
> > help me to understand this point:
> > For "projfrac =0" I expect the surface based analysis to
> > be running close to white matter. Right? and when I used
> > "projfrac=0.5" the analysis is running in the middle area between pial
> > and white. When the analysis is not showing any differne between the
> > groups for "projfrac 0.5" and showing differnce for "projfrac 0" that
> > means the differnce between the groups is deeper and closer to white
> > matter. Is this correct?
> > Thank you for any input and clarification!
> > Bests,
> > John
> > *Sent:* Tuesday, January 10, 2017 at 10:51 AM
> > *From:* "Douglas Greve" 
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> >
> > When you say in the corpus callosum, do you mean in WM? The
> > surface-based analysis is only for cortical GM. If you mean in GM near
> > the CC, then the analysis is appropriate. The projfrac parameter sets
> > the sampling location between the white and pial surfaces where 0.5
> > means half way.
> >
> > On 1/10/17 8:07 AM, John Anderson wrote:
> >
> > Dear FS experts,
> > I am working on surface based analysis using freesurfer. I want to
> > inquire about the flag "projfrac" in the command "mris_preproc"
> > I ran voxel wise analysis including the same subjects. I found
> > differnce between the groups in areas close to the corpus
> > callosum. I want to get the same results using surface based
> > analysis. If I use the projfrac=0.5 is this able to show the same
> > results that I got in voxel wise analysis at the level of the
> > corpus callosum. Do I need to use differnt number for projfrac ?
> > Thank you for any advice.
> >
> > Best,
> > John
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___ 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
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 

Re: [Freesurfer] QDEC table import issue

[Paul Rowley]

It was the spaces! Thanks for the help
On Jan 13, 2017, at 11:40 AM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:

I'm not sure that QDEC can read in a CSV file. Can you remove the commas
and try again? You'll also have to remove the spaces between column headings


On 01/13/2017 10:55 AM, Paul Rowley wrote:
Good morning,
I’m experiencing issues importing data into QDEC. When I upload the table, this 
is the error I receive:
Loading data table /Applications/freesurfer/subjects/qdec/qdec.table.dat...
Number of columns:  10
fsid column:1
Number of factors:  9
Number of subjects: 19
ERROR: QdecSubject::GetContinuousFactor failure: could not find factor name: 
L_temporalpole_thickavg for subject NV_002_V1

I’ve attached the table and would greatly appreciate any advice on resolving 
this issue.
Thanks in advance for your help,
Paul


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: 
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

___
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] QDEC table import issue

[Douglas N Greve]

I'm not sure that QDEC can read in a CSV file. Can you remove the commas 
and try again? You'll also have to remove the spaces between column headings


On 01/13/2017 10:55 AM, Paul Rowley wrote:
> Good morning,
> I’m experiencing issues importing data into QDEC. When I upload the table, 
> this is the error I receive:
> Loading data table /Applications/freesurfer/subjects/qdec/qdec.table.dat...
> Number of columns:  10
> fsid column:1
> Number of factors:  9
> Number of subjects: 19
> ERROR: QdecSubject::GetContinuousFactor failure: could not find factor name: 
> L_temporalpole_thickavg for subject NV_002_V1
>
> I’ve attached the table and would greatly appreciate any advice on resolving 
> this issue.
> Thanks in advance for your help,
> Paul
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] surface based analysis (projfrac)

[Douglas N Greve]

On 01/12/2017 05:20 PM, John Anderson wrote:
> Thank you very much Doug and thank you for briniging the issue of 
> "partial volume effect " to my attention. Kindly, I have one last 
> question.
> I found in wiki that the default values for projfrc value are between 
> 0 and 1. Are there negative values? I mean for example "-2, -1, 0 , 1, 
> 2 ", In other words, less than zero means the surface based analysis 
> is running at a lower level of the white matter.
Yes
> Can the issue of the partial volume effect be avoided by using larger 
> numbers for "projfrac" ?
No, PVEs can't be avoided that way.
> Bests,
> John
> *Sent:* Thursday, January 12, 2017 at 5:08 PM
> *From:* "Douglas N Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> yes, that is correct. However, understand that there might only be a
> difference of 1mm between those two locations, so it could easily be a
> partial volume effect
>
>
> On 01/11/2017 08:50 AM, John Anderson wrote:
> > Thank you Doug,
> > Exactly! I meant GM near the CC.
> > When I used "projfrac=0.5 " there was no differnce between the groups
> > at "cwp 0.05", and when I changed the "projfrac to 0" I got
> > significant differnce between the groups in specific areas at "cwp
> > 0.01". Kindly, how can this be explained? I highly appreciate if you
> > help me to understand this point:
> > For "projfrac =0" I expect the surface based analysis to
> > be running close to white matter. Right? and when I used
> > "projfrac=0.5" the analysis is running in the middle area between pial
> > and white. When the analysis is not showing any differne between the
> > groups for "projfrac 0.5" and showing differnce for "projfrac 0" that
> > means the differnce between the groups is deeper and closer to white
> > matter. Is this correct?
> > Thank you for any input and clarification!
> > Bests,
> > John
> > *Sent:* Tuesday, January 10, 2017 at 10:51 AM
> > *From:* "Douglas Greve" 
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] surface based analysis (projfrac)
> >
> > When you say in the corpus callosum, do you mean in WM? The
> > surface-based analysis is only for cortical GM. If you mean in GM near
> > the CC, then the analysis is appropriate. The projfrac parameter sets
> > the sampling location between the white and pial surfaces where 0.5
> > means half way.
> >
> > On 1/10/17 8:07 AM, John Anderson wrote:
> >
> > Dear FS experts,
> > I am working on surface based analysis using freesurfer. I want to
> > inquire about the flag "projfrac" in the command "mris_preproc"
> > I ran voxel wise analysis including the same subjects. I found
> > differnce between the groups in areas close to the corpus
> > callosum. I want to get the same results using surface based
> > analysis. If I use the projfrac=0.5 is this able to show the same
> > results that I got in voxel wise analysis at the level of the
> > corpus callosum. Do I need to use differnt number for projfrac ?
> > Thank you for any advice.
> >
> > Best,
> > John
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___ 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
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
> 
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> 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.har

Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream

[Tamara Tavares]

Hi Martin,

Thank you for the clarification. I assume this participant should be
removed?  As a rule of thumb, should I exclude participants who have a
total of 3% scaling? Is there a way to check potential scaling problems
(e.g. looking into the recon-all.log to see scaling or checking alignment
between the longitudinal time points)?

Thank you again for your help.

Best,
Tamara

Message: 7
Date: Thu, 12 Jan 2017 16:20:11 +0100
From: Martin Reuter 
Subject: Re: [Freesurfer] Brighter image at baseline vs. follow up
using   longitudinal processing stream
To: Freesurfer support list 
Message-ID: <2d4d7b7c-9915-454c-9a41-aa9fde9d3...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="us-ascii"

Hi Tamara,

that information is in the screen output:


 Determinant : 1.03358


also
Scale = diag([  1.0109774487584  1.0113715685396  1.0108915357302  ])

so it finds some scaling (approx 1% in each axis direction, so a total of
3%). This can happen in individual cases, but if it is consistent I would
be worried.

Best, Martin


> On 11 Jan 2017, at 21:21, Tamara Tavares  wrote:
>
> Hi Dr. Reuter.
>
> Thank you again for your help.
>
> I ran the following command: "mri_robust_register --mov rawavg_1.mgz
--dst rawavg_2.mgz --lta v1to2.lta --affine --satit" on the two rawavg.mgz
images; one from each time point from the cross-sectional outputs. I have
attached the information from the terminal and the output. Are these
outputs appropriate to find the scaling information? If so, where can I
find it? I am not very familiar with transformations, thus any information
or directions to resources I can use would be very much appreciated.
>
> Thank you in advance for you help.
>
> Best,
> Tamara
___
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] QDEC table import issue

[Paul Rowley]

Good morning,
I’m experiencing issues importing data into QDEC. When I upload the table, this 
is the error I receive: 
Loading data table /Applications/freesurfer/subjects/qdec/qdec.table.dat...
Number of columns:  10
fsid column:1
Number of factors:  9
Number of subjects: 19
ERROR: QdecSubject::GetContinuousFactor failure: could not find factor name: 
L_temporalpole_thickavg for subject NV_002_V1

I’ve attached the table and would greatly appreciate any advice on resolving 
this issue. 
Thanks in advance for your help,
Paul 


qdec.table.dat
Description: qdec.table.dat
___
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 in FreeSurfer 6.0 trac-paths error

[Yendiki, Anastasia]

Hi Derek - Thanks for testing the 6.0 release candidate. Does it keep running 
after this message? Since this is a warning and not an error, it may not be 
critical. If you run mri_info on your dwi.nii.gz, does the TE show up as zero?

Best,
a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Derek A Pisner 
[dpis...@utexas.edu]
Sent: Thursday, January 12, 2017 10:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA in FreeSurfer 6.0 trac-paths error


Hi Anastasia,

I am getting the following error when running trac-all –paths on all of my 
diffusion images using the newly updated TRACULA:

vlogin03.ls5(97)$ 
/work/04171/dpisner/stampede/Applications/freesurfer/bin/trac-all -no-isrunning 
-path -c 
/work/04171/dpisner/data/ABM/TRACULA/tractography_output/s002/trac_config.txt

niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm

WARNING: niiRead(): unknown time units 0 in 
/work/04171/dpisner/data/ABM/TRACULA/tractography_output/s002/dmri/dwi.nii.gz



Any idea what’s going on here?



Thanks as always,

Derek Pisner
Doctoral Student
CLA 4.600
Mood Disorders Laboratory (MDL)
Department of Psychology | The University of Texas at Austin



P.S. Here is the header information on my dwi.nii.gz file:
vlogin03.ls5(105)$ fslhd dwi.nii.gz
filename   dwi.nii.gz
sizeof_hdr 348
data_type  FLOAT32
dim0   4
dim1   115
dim2   115
dim3   56
dim4   55
dim5   1
dim6   1
dim7   1
vox_units  Unknown
time_units Unknown
datatype   16
nbyper 4
bitpix 32
pixdim00.00
pixdim12.00
pixdim22.00
pixdim32.00
pixdim41.00
pixdim51.00
pixdim61.00
pixdim71.00
vox_offset 352
cal_max0.
cal_min0.
scl_slope  1.00
scl_inter  0.00
phase_dim  0
freq_dim   0
slice_dim  0
slice_name Unknown
slice_code 0
slice_start0
slice_end  0
slice_duration 0.00
time_offset0.00
intent Unknown
intent_code0
intent_name
intent_p1  0.00
intent_p2  0.00
intent_p3  0.00
qform_name Unknown
qform_code 0
qto_xyz:1  2.00  0.00  0.00  0.00
qto_xyz:2  0.00  2.00  0.00  0.00
qto_xyz:3  0.00  0.00  2.00  0.00
qto_xyz:4  0.00  0.00  0.00  1.00
qform_xorient  Left-to-Right
qform_yorient  Posterior-to-Anterior
qform_zorient  Inferior-to-Superior
sform_name Aligned Anat
sform_code 2
sto_xyz:1  -2.00  0.00  0.00  114.551003
sto_xyz:2  0.00  2.00  0.00  -74.456001
sto_xyz:3  0.00  0.00  2.00  -0.960182
sto_xyz:4  0.00  0.00  0.00  1.00
sform_xorient  Right-to-Left
sform_yorient  Posterior-to-Anterior
sform_zorient  Inferior-to-Superior
file_type  NIFTI-1+
file_code  1
descrip

aux_file

--
Derek Pisner
___
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] -cw256 and -hires

[Bruce Fischl]

Hi Chris

are you talking about recon-all -hires ...? That has worked for me without 
cropping to 256.


cheers
Bruce


On Fri, 13 Jan 2017, Chris Adamson wrote:



In the git version I’m trying to use the -hires option on an image. It
initially says that I need the cw256 option to restrict the FOV to 256. I
tried this but initially it did nothing and then when I edited recon-all it
add –cw256 to the mri_convert command to create orig.mgz but the same error
about the FOV came up. Any thoughts?

 

Chris.

 

Dr Chris Adamson

Senior Research Officer

Developmental Imaging, Clinical Sciences

 

Murdoch Childrens Research Institute

The Royal Children’s Hospital

Flemington Road, Parkville, VIC 3052 Australia

E chris.adam...@mcri.edu.au 

www.mcri.edu.au

 

 

This e-mail and any attachments to it (the "Communication") are, unless
otherwise stated, confidential, may contain copyright material and is for
the use only of the intended recipient. If you receive the Communication in
error, please notify the sender immediately by return e-mail, delete the
Communication and the return e-mail, and do not read, copy, retransmit or
otherwise deal with it. Any views expressed in the Communication are those
of the individual sender only, unless expressly stated to be those of
Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its
related entities. MCRI does not accept liability in connection with the
integrity of or errors in the Communication, computer virus, data
corruption, interference or delay arising from or in respect of the
Communication.

 

P Please consider the environment before printing this email

 


__
This email has been scanned by the Symantec Email Security.cloud service.
For more information please visit http://www.symanteccloud.com
__

___
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] Reviewer questions...

[Iglesias Gonzalez, Eugenio]

Thanks for your good points, Antonin.

More on the matter:

When segmenting standard resolution (~ 1mm) T1 scans, the position of the 
internal boundaries between the hippocampal substructures largely relies on 
prior knowledge acquired from our ex vivo training data and summarized in our 
statistical atlas. Therefore, the volumes of subfields around these boundaries 
(especially internal subfields such as the GC-DG and molecular layer) must be 
interpreted with caution, and further validation with higher resolution data 
should be carried out to confirm the results.

 Having said that:

1. The fimbria is visible in 1 mm T1 data. It is true that, being a thin 
structure, its volume might be affected by motion artifacts more than that of 
other structures (see our Neuroimage paper linked by Antonin).

2. The hippocampus / amygdala interface is given by the alveus, which is a very 
thin structure, yielding a very faint (but not invisible) boundary in 1mm data, 
particularly if the scan is affected by motion. For that reason, automated 
methods sometimes make mistakes in that area, but they mostly get it right, 
partly thanks to the prior knowledge encoded in atlases.

3. The tail relies on geometric criteria for the anterior / posterior cut-off, 
but does not attempt to infer any internal boundaries, so it is definitely 
reliable even when segmented from 1 mm scans.

Jerome, for your specific case:

- The tail should not be problematic, for reason 3 above.
- Schoemaker’s article, in addition to using an ancient version of FreeSurfer,  
is about segmentation of infant MRI, which is more difficult that segmenting 
adults.
- Volumetric protocol: see Table 2 of our Neuroimage paper describing the 
hippocampal atlas. For the tail: “we identified the first coronal slice 
(anterior to posterior) where the fornix is fully connected to the hippocampus, 
and labeled the whole hippocampus with this “umbrella” label in the remaining 
slices”.
- The fimbria is visible (reason 1 above).
- The molecular layer is not visible at 1 mm resolution, but you can still get 
and idea of its volume thanks to the prior - again, results based on such 
volumes should be interpreted with caution. However, if I understood correctly, 
your results are on the tail, and hence reliable (point 3).

I hope this helps.

Kind regards, and sorry for the long response!

/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 13 Jan 2017, at 01:23, Antonin Skoch mailto:a...@ikem.cz>> 
wrote:

Dear Jerome,

I think I could chime in with my opinion: The Schoemaker et al paper results 
are based on hippocampus/amygdala segmentations in FreeSurfer 4.4.

Hippocampal subfields segmentation module from development version you used 
should be more precise than 4.4. version and also the anatomical landmarks are 
well specified in paper Iglesias et al, 2015:

https://www.ncbi.nlm.nih.gov/pubmed/25936807
I think this paper can be used as a good basis for arguments to your reviewer.

Concerning the reliability of estimation of particular hippocampal subfields, I 
think it also depend on what resolution was your input images, and whether you 
used additional high-resolution T2. The effect of various image resolution on 
the reliability of results is also well discussed in above-mentioned paper I 
think.

Regards,

Antonin Skoch

___
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.

[Freesurfer] Covariates / rmANOVA

[Gracien, Rene-Maxime]

Hello,

we are trying to use covariates while calculating a rmANOVA as described in 
https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova. Is this 
technically possible with freesurfer?

Thank you, best regards, René
___
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.