Re: [Freesurfer] Extracting structural measures from trend-level PET clusters

[Elijah Mak]

Hi,

A bit more info: the stack of thickness maps consists of
lh.thickness.fwhm15.fsaverage.mghs that were created after -qcache. I used
mri_concat --f --o to create the stack of mghs.  I also noticed that the
vertex values are in the range of 20-30, whereas those in the
lh.thickness.fsvaerage mghs are in the expected range.

Should I be using this for the calculation of the thickness in the clusters
instead?

Best Wishes,
Elijah

On Sat, Nov 12, 2016 at 12:15 AM, Elijah Mak 
wrote:

> Thanks, Doug.
>
> It works but I am not sure if the values I'm getting are correct. Is this
> supposed to be reporting the mean cortical thickness of each cluster? I
> have pasted the output below from the avgwf below.  The names of the
> clusters correspond to the regions from the "summary" text, am I right?
>
>
> Group lh_fusiform lh_precentral lh_insular lh_precuneus lh_parsorbitalis
> 1 24.29454 29.53935 14.24736 28.97924 31.54577
> 1 25.68872 28.26156 17.47828 28.20604 30.38902
> 2 25.46281 30.75879 19.34943 29.59019 32.0404
> 2 25.55514 27.23871 17.27937 29.14274 29.75657
>
> Another related question: Is it possible to simply take the mean cortical
> thickness across the voxels exceeding p<0.001 from the uncorrected sig.mgh?
>
> Thanks again!
>
> Best Wishes,
> Elijah
>
>


-- 

Elijah Mak, Gates Scholar

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ
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Re: [Freesurfer] Extracting structural measures from trend-level PET clusters

[Elijah Mak]

Thanks, Doug.

It works but I am not sure if the values I'm getting are correct. Is this
supposed to be reporting the mean cortical thickness of each cluster? I
have pasted the output below from the avgwf below.  The names of the
clusters correspond to the regions from the "summary" text, am I right?


Group lh_fusiform lh_precentral lh_insular lh_precuneus lh_parsorbitalis
1 24.29454 29.53935 14.24736 28.97924 31.54577
1 25.68872 28.26156 17.47828 28.20604 30.38902
2 25.46281 30.75879 19.34943 29.59019 32.0404
2 25.55514 27.23871 17.27937 29.14274 29.75657

Another related question: Is it possible to simply take the mean cortical
thickness across the voxels exceeding p<0.001 from the uncorrected sig.mgh?

Thanks again!

Best Wishes,
Elijah
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Re: [Freesurfer] recon all

[John Anderson]

Thank you very much Doug,

Kindly, what do you suggest me to use instead of fslswapidim. What is your choice in this case? I highly appreciate your experience !
 

Bests,
John


 

Sent: Friday, November 11, 2016 at 4:42 PM
From: "Douglas N Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon all

On this volume as the head is almost at a 45deg angle perhaps causing
the nominal SI and AP to swap. Even after swap dim, the angle is pretty
extreme, but maybe better than the original so the tal check does not
fail. In general, I don't like to use swapdim as I'm afraid that it
might left-right rev the volume. In either case, you can manually check
the tal reg to see if it looks ok.


On 11/11/2016 03:56 PM, John Anderson wrote:
> Thank you Doug,
> Attched are to snapshots
> #1 is for the original T1 ( i.e. as aquired) and this image what
> output the error message mentioned in my previous email.
> #2 is after correcting the orientation using the command "*fslswapdim
> 001.nii RL PA IS T1-2mm_orientOK.nii"*
> I re run the same command "recon-all" on the newly corrected T1 image.
> The analysis is runnig fine right now, but when I checked the file
> "recon-all" I found similar error to what terminated my previous
> analysis. The differnce here is that the analysis didn't fail!
> Here is what I have in "recon.log"
> talairach_afd -T 0.005 -xfm transforms/talairach.xfm
> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
> ***FAILED*** (p=0.0386, pval=0.0034 < threshold=0.0050)
> INFO: Attempting MINC mritotal to perform Talairach align
> Do I need to warry about this error? I appreciate any suggestion to
> improve analyzing this image.
> Bests,
> John
> *Sent:* Friday, November 11, 2016 at 3:19 PM
> *From:* "Douglas N Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] recon all
> This can also happen if the head is oriented in a strange way. This can
> happen with older patients that tend to tilt their head back.
>
>
> On 11/10/2016 08:27 PM, Bruce Fischl wrote:
> > Hi John
> >
> > it means that the talairach transform that was computed was extremely
> > unlikely and deemed to be probably incorrect. Frequently this happens
> > if you start with images (like analyze) that don't contain accurate
> > direction cosine information. You can check this by bringing one of
> > the volumes in freeview and checking to make sure that the anatomical
> > directions we show
> > (e.g. anterior/posterior) correspond to the true anatomy. Sometimes
> > abnormal anatomiies like huge ventricles can also make it fail, but
> > you need to figure out which one it is before deciding what to do
> >
> > cheers
> > Bruce
> >
> >
> > On Fri, 11 Nov 2016, John Anderson wrote:
> >
> >> Dear Freesurfer experts,
> >> I ran the following command on a T1 image
> >> recon-all -subjid 089 -all -qcache
> >>
> >> and I got the following error message:
> >>
> >> talairach_afd -T 0.005 -xfm transforms/talairach.xfm
> >>
> >> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
> >> ***FAILED*** (p=0.0344, pval=0.0034 < threshold=0.0050)
> >>
> >>
> >> I highly appreciate an explanation for the meaning of this error and
> >> how to
> >> fix it.
> >>
> >>
> >> Best
> >> John
> >>
> >>
> >
> >
> > ___
> > 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/
>
> ___
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>
>
> 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
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> dispose of the e-mail.
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--
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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
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Re: [Freesurfer] recon all

[Douglas N Greve]

I don't think that you need to do anything. If the tal reg checks out 
ok, then you can turn off the check when you  run recon-all by adding 
-no-tal-check



On 11/11/2016 05:40 PM, John Anderson wrote:
> Thank you very much Doug,
> Kindly, what do you suggest me to use instead of fslswapidim. What is 
> your choice in this case? I highly appreciate your experience !
> Bests,
> John
> *Sent:* Friday, November 11, 2016 at 4:42 PM
> *From:* "Douglas N Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] recon all
> On this volume as the head is almost at a 45deg angle perhaps causing
> the nominal SI and AP to swap. Even after swap dim, the angle is pretty
> extreme, but maybe better than the original so the tal check does not
> fail. In general, I don't like to use swapdim as I'm afraid that it
> might left-right rev the volume. In either case, you can manually check
> the tal reg to see if it looks ok.
>
>
> On 11/11/2016 03:56 PM, John Anderson wrote:
> > Thank you Doug,
> > Attched are to snapshots
> > #1 is for the original T1 ( i.e. as aquired) and this image what
> > output the error message mentioned in my previous email.
> > #2 is after correcting the orientation using the command "*fslswapdim
> > 001.nii RL PA IS T1-2mm_orientOK.nii"*
> > I re run the same command "recon-all" on the newly corrected T1 image.
> > The analysis is runnig fine right now, but when I checked the file
> > "recon-all" I found similar error to what terminated my previous
> > analysis. The differnce here is that the analysis didn't fail!
> > Here is what I have in "recon.log"
> > talairach_afd -T 0.005 -xfm transforms/talairach.xfm
> > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
> > ***FAILED*** (p=0.0386, pval=0.0034 < threshold=0.0050)
> > INFO: Attempting MINC mritotal to perform Talairach align
> > Do I need to warry about this error? I appreciate any suggestion to
> > improve analyzing this image.
> > Bests,
> > John
> > *Sent:* Friday, November 11, 2016 at 3:19 PM
> > *From:* "Douglas N Greve" 
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] recon all
> > This can also happen if the head is oriented in a strange way. This can
> > happen with older patients that tend to tilt their head back.
> >
> >
> > On 11/10/2016 08:27 PM, Bruce Fischl wrote:
> > > Hi John
> > >
> > > it means that the talairach transform that was computed was extremely
> > > unlikely and deemed to be probably incorrect. Frequently this happens
> > > if you start with images (like analyze) that don't contain accurate
> > > direction cosine information. You can check this by bringing one of
> > > the volumes in freeview and checking to make sure that the anatomical
> > > directions we show
> > > (e.g. anterior/posterior) correspond to the true anatomy. Sometimes
> > > abnormal anatomiies like huge ventricles can also make it fail, but
> > > you need to figure out which one it is before deciding what to do
> > >
> > > cheers
> > > Bruce
> > >
> > >
> > > On Fri, 11 Nov 2016, John Anderson wrote:
> > >
> > >> Dear Freesurfer experts,
> > >> I ran the following command on a T1 image
> > >> recon-all -subjid 089 -all -qcache
> > >>
> > >> and I got the following error message:
> > >>
> > >> talairach_afd -T 0.005 -xfm transforms/talairach.xfm
> > >>
> > >> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
> > >> ***FAILED*** (p=0.0344, pval=0.0034 < threshold=0.0050)
> > >>
> > >>
> > >> I highly appreciate an explanation for the meaning of this error and
> > >> how to
> > >> fix it.
> > >>
> > >>
> > >> Best
> > >> John
> > >>
> > >>
> > >
> > >
> > > ___
> > > 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 

[Freesurfer] How to view overlapping voxels across multiple sig.mgh files?

[Elijah Mak]

Hi Freesurfer Team,

I am just wondering if there is a neat way to derive .mgh files containing
cluster information about spatially overlapping voxels across various
sig.mgh?

Thank you.

Best Wishes,
Elijah
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Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

[Matthieu Vanhoutte]

Is it better to compute mean to weight by number of vertices or surface
area ?

Best,
Matthieu

Le 11 nov. 2016 11:33 PM, "Douglas N Greve"  a
écrit :

> Vertices do not have equal areas and are not equally spaced
>
>
> On 11/11/2016 05:11 PM, Matthieu Vanhoutte wrote:
> >
> > Thank you Douglas for giving me a way to compute area from segmented
> > surface data.
> >
> > Are vertices equally spaced along cortex or do triangles all have same
> > area ?
> >
> > Best,
> > Matthieu
> >
> >
> > Le 11 nov. 2016 10:55 PM, "Douglas N Greve"  > > a écrit :
> >
> > If you want to do it on fsaverage, then
> >
> > mris_segstats --i $SUBJECTS/fsaverage/surf/lh.white.avg.area.mgh
> --seg
> > lh.sign_clust.bin.mgh
> > --excludeid 0 --sum lh.bin.area.sum --accumulate
> >
> >
> >
> >
> > On 11/11/2016 04:48 PM, Matthieu Vanhoutte wrote:
> > >
> > > Dear Douglas,
> > >
> > > Yes I would like to in order to compute mean of some means.
> > Maybe not
> > > if it is equivalent to number of vertices (are vertices distributed
> > > equaly distant on the cortical surface ?)
> > >
> > > In case I need surface area, do I have to convert overlay to
> > > annotation file to be used with mri_segstats ?
> > >
> > > Best regards,
> > > Matthieu
> > >
> > >
> > > Le 11 nov. 2016 9:21 PM, "Douglas N Greve"
> > 
> > >  > >> a écrit :
> > >
> > > NVox is the number of vertices. The Volume_mm3 is not
> > meaningful.
> > > Do you
> > > want area?
> > >
> > >
> > > On 11/11/2016 04:53 AM, Matthieu Vanhoutte wrote:
> > > > Dear Douglas,
> > > >
> > > > I come back to you concerning stats made from binary .mgh
> > > surface data
> > > > file:
> > > >
> > > > mri_segstats --i lh.fsaverage.sm10.mgh --seg
> > lh.sign_clust.bin.mgh
> > > > --excludeid 0 --sum lh.bin.sum --avgwf lh.wav.bin.txt
> > > >
> > > > In the output file « lh.bin.sum » all is considered as volume
> > > > input/output as you could see below:
> > > >
> > > > /# InVolFileTimeStamp  2016/04/28 09:46:19 /
> > > > /# InVolFrame 0 /
> > > > /# ExcludeSegId 0 /
> > > > /# Only reporting non-empty segmentations/
> > > > /# VoxelVolume_mm3 1 /
> > > > /# TableCol  1 ColHeader Index /
> > > > /# TableCol  1 FieldName Index /
> > > > /# TableCol  1 Units NA /
> > > > /# TableCol  2 ColHeader SegId /
> > > > /# TableCol  2 FieldName Segmentation Id/
> > > > /# TableCol  2 Units NA/
> > > > /# TableCol  3 ColHeader NVoxels /
> > > > /# TableCol  3 FieldName Number of Voxels/
> > > > /# TableCol  3 Units unitless/
> > > > /# TableCol  4 ColHeader Volume_mm3/
> > > > /# TableCol  4 FieldName Volume/
> > > > /# TableCol  4 Units mm^3/
> > > > /# TableCol  5 ColHeader Mean /
> > > > /# TableCol  5 FieldName Intensity Mean/
> > > > /# TableCol  5 Units unknown/
> > > > /# TableCol  6 ColHeader StdDev/
> > > > /# TableCol  6 FieldName Itensity StdDev/
> > > > /# TableCol  6 Units unknown/
> > > > /# TableCol  7 ColHeader Min/
> > > > /# TableCol  7 FieldName Intensity Min/
> > > > /# TableCol  7 Units unknown/
> > > > /# TableCol  8 ColHeader Max/
> > > > /# TableCol  8 FieldName Intensity Max/
> > > > /# TableCol  8 Units unknown/
> > > > /# TableCol  9 ColHeader Range/
> > > > /# TableCol  9 FieldName Intensity Range/
> > > > /# TableCol  9 Units unknown/
> > > > /# NRows 1 /
> > > > /# NTableCols 9 /
> > > > /# ColHeaders  Index SegId NVoxels Volume_mm3 StructName
> > Mean StdDev
> > > > Min Max Range /
> > > > /  1   1 1151011510.0  Seg0001  7.6819  1.4396
> > > > 4.486210.9042 6.4180 /
> > > >
> > > > As my inputs are all surface data could I consider that
> > NVoxels is
> > > > equal to NVertices and Volume_mm3 is equal to
> > SurfaceArea_mm2 ?
> > > >
> > > > Best regards,
> > > > Matthieu
> > > >
> > > >> Le 10 nov. 2016 à 23:18, Matthieu Vanhoutte
> > > >>  > 
> > >  > >
> > >  > 
> > >  > 

Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple input scans

[Douglas N Greve]

I guess I'm not sure what the problem is. If you need to go from a 
surface coordinate to scanner coord, then get the tkr2scanner matrix and 
multiply it by the surface coord. The volumes are not transformed to tkr 
coords. The various xform matrices are kept with the volume. What are 
you trying to do?


On 11/11/2016 04:59 PM, Krieger, Donald N. wrote:
> Now I don't understand.
>
> Here's the situation:
> Someone has given me a bunch of MEG's with freesurfer runs which were run 
> using both a T1 and a T2 scan with -T2pial .
>   Mri_info --tkr2scanner gives the same transform for aparac+aseg.mgz, 
> T1.mgz, and T2.mgz  .
> I will be coregistering the MEG which comes with each T1/T2 pair .
> Since I'm getting the same transform from all the .mgz's, I speculated that 
> freesurfer transformed both scans to tkr coordinates, did its thing, and then 
> picked the T1 to provide the tkr2scanner transform.
> ???
>
> Don
>
>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
>> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
>> Sent: Friday, November 11, 2016 4:35 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mri_info --tkr2scanner result for run with 
>> multiple input
>> scans
>>
>> If the head has not moved, then they will share a scanner RAS, ie,  a given
>> scanner RAS will be at the same place in the head in the two scans, though 
>> they
>> will map to different col,row,slice in their respective volumes. If the head 
>> has
>> moved, then you will need to perform a registration to get them aligned.
>>
>>
>> On 11/11/2016 04:17 PM, Krieger, Donald N. wrote:
>>> Thanks for getting back, Doug.
>>> I understand - but if there are two scans, aren't there two scanner RAS's 
>>> since
>> the head presumably moved at least a little from one to the other or the 
>> scans
>> could have been done on different scanners?
>>> Don
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Friday, November 11, 2016 3:22 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] mri_info --tkr2scanner result for run with
>>> multiple input scans
>>>
>>> -tkr2scanner gives the transform that takes "tkregister RAS" and
>>> converts it to scanner RAS. "tkregisterRAS" is the RAS system used by
>>> surfaces (it, a vertex xyz is in tkregisterRAS). See
>>> http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
>>>
>>>
>>>
>>> On 11/10/2016 09:33 PM, Krieger, Donald N. wrote:
 If I run recon-all with both a T1 and a T2 scan and switch t2pial,
 does mri_info -tkr2scanner give me the transform to the T1 scanner
 frame of reference?

 And if I run recon-all with many T1's , what does mri_info
 -tkr2scanner give me then?

 Thanks - Don



 ___
 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
>>>
>>>
>> --
>> 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
> 

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

[Douglas N Greve]

Vertices do not have equal areas and are not equally spaced


On 11/11/2016 05:11 PM, Matthieu Vanhoutte wrote:
>
> Thank you Douglas for giving me a way to compute area from segmented 
> surface data.
>
> Are vertices equally spaced along cortex or do triangles all have same 
> area ?
>
> Best,
> Matthieu
>
>
> Le 11 nov. 2016 10:55 PM, "Douglas N Greve"  > a écrit :
>
> If you want to do it on fsaverage, then
>
> mris_segstats --i $SUBJECTS/fsaverage/surf/lh.white.avg.area.mgh --seg
> lh.sign_clust.bin.mgh
> --excludeid 0 --sum lh.bin.area.sum --accumulate
>
>
>
>
> On 11/11/2016 04:48 PM, Matthieu Vanhoutte wrote:
> >
> > Dear Douglas,
> >
> > Yes I would like to in order to compute mean of some means.
> Maybe not
> > if it is equivalent to number of vertices (are vertices distributed
> > equaly distant on the cortical surface ?)
> >
> > In case I need surface area, do I have to convert overlay to
> > annotation file to be used with mri_segstats ?
> >
> > Best regards,
> > Matthieu
> >
> >
> > Le 11 nov. 2016 9:21 PM, "Douglas N Greve"
> 
> >  >> a écrit :
> >
> > NVox is the number of vertices. The Volume_mm3 is not
> meaningful.
> > Do you
> > want area?
> >
> >
> > On 11/11/2016 04:53 AM, Matthieu Vanhoutte wrote:
> > > Dear Douglas,
> > >
> > > I come back to you concerning stats made from binary .mgh
> > surface data
> > > file:
> > >
> > > mri_segstats --i lh.fsaverage.sm10.mgh --seg
> lh.sign_clust.bin.mgh
> > > --excludeid 0 --sum lh.bin.sum --avgwf lh.wav.bin.txt
> > >
> > > In the output file « lh.bin.sum » all is considered as volume
> > > input/output as you could see below:
> > >
> > > /# InVolFileTimeStamp  2016/04/28 09:46:19 /
> > > /# InVolFrame 0 /
> > > /# ExcludeSegId 0 /
> > > /# Only reporting non-empty segmentations/
> > > /# VoxelVolume_mm3 1 /
> > > /# TableCol  1 ColHeader Index /
> > > /# TableCol  1 FieldName Index /
> > > /# TableCol  1 Units NA /
> > > /# TableCol  2 ColHeader SegId /
> > > /# TableCol  2 FieldName Segmentation Id/
> > > /# TableCol  2 Units NA/
> > > /# TableCol  3 ColHeader NVoxels /
> > > /# TableCol  3 FieldName Number of Voxels/
> > > /# TableCol  3 Units unitless/
> > > /# TableCol  4 ColHeader Volume_mm3/
> > > /# TableCol  4 FieldName Volume/
> > > /# TableCol  4 Units mm^3/
> > > /# TableCol  5 ColHeader Mean /
> > > /# TableCol  5 FieldName Intensity Mean/
> > > /# TableCol  5 Units unknown/
> > > /# TableCol  6 ColHeader StdDev/
> > > /# TableCol  6 FieldName Itensity StdDev/
> > > /# TableCol  6 Units unknown/
> > > /# TableCol  7 ColHeader Min/
> > > /# TableCol  7 FieldName Intensity Min/
> > > /# TableCol  7 Units unknown/
> > > /# TableCol  8 ColHeader Max/
> > > /# TableCol  8 FieldName Intensity Max/
> > > /# TableCol  8 Units unknown/
> > > /# TableCol  9 ColHeader Range/
> > > /# TableCol  9 FieldName Intensity Range/
> > > /# TableCol  9 Units unknown/
> > > /# NRows 1 /
> > > /# NTableCols 9 /
> > > /# ColHeaders  Index SegId NVoxels Volume_mm3 StructName
> Mean StdDev
> > > Min Max Range /
> > > /  1   1 1151011510.0  Seg0001  7.6819  1.4396
> > > 4.486210.9042 6.4180 /
> > >
> > > As my inputs are all surface data could I consider that
> NVoxels is
> > > equal to NVertices and Volume_mm3 is equal to
> SurfaceArea_mm2 ?
> > >
> > > Best regards,
> > > Matthieu
> > >
> > >> Le 10 nov. 2016 à 23:18, Matthieu Vanhoutte
> > >>  
> >  >
> >  
> >   > >> écrit :
> > >>
> > >> Thank you Douglas !
> > >>
> > >>
> > >> Le 10 nov. 2016 7:21 PM, "Douglas N Greve"
> >  
> >
> > >>  
> > 

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

[Matthieu Vanhoutte]

Thank you Douglas for giving me a way to compute area from segmented
surface data.

Are vertices equally spaced along cortex or do triangles all have same area
?

Best,
Matthieu

Le 11 nov. 2016 10:55 PM, "Douglas N Greve"  a
écrit :

If you want to do it on fsaverage, then

mris_segstats --i $SUBJECTS/fsaverage/surf/lh.white.avg.area.mgh --seg
lh.sign_clust.bin.mgh
--excludeid 0 --sum lh.bin.area.sum --accumulate




On 11/11/2016 04:48 PM, Matthieu Vanhoutte wrote:
>
> Dear Douglas,
>
> Yes I would like to in order to compute mean of some means. Maybe not
> if it is equivalent to number of vertices (are vertices distributed
> equaly distant on the cortical surface ?)
>
> In case I need surface area, do I have to convert overlay to
> annotation file to be used with mri_segstats ?
>
> Best regards,
> Matthieu
>
>
> Le 11 nov. 2016 9:21 PM, "Douglas N Greve"  > a écrit :
>
> NVox is the number of vertices. The Volume_mm3 is not meaningful.
> Do you
> want area?
>
>
> On 11/11/2016 04:53 AM, Matthieu Vanhoutte wrote:
> > Dear Douglas,
> >
> > I come back to you concerning stats made from binary .mgh
> surface data
> > file:
> >
> > mri_segstats --i lh.fsaverage.sm10.mgh --seg lh.sign_clust.bin.mgh
> > --excludeid 0 --sum lh.bin.sum --avgwf lh.wav.bin.txt
> >
> > In the output file « lh.bin.sum » all is considered as volume
> > input/output as you could see below:
> >
> > /# InVolFileTimeStamp  2016/04/28 09:46:19 /
> > /# InVolFrame 0 /
> > /# ExcludeSegId 0 /
> > /# Only reporting non-empty segmentations/
> > /# VoxelVolume_mm3 1 /
> > /# TableCol  1 ColHeader Index /
> > /# TableCol  1 FieldName Index /
> > /# TableCol  1 Units NA /
> > /# TableCol  2 ColHeader SegId /
> > /# TableCol  2 FieldName Segmentation Id/
> > /# TableCol  2 Units NA/
> > /# TableCol  3 ColHeader NVoxels /
> > /# TableCol  3 FieldName Number of Voxels/
> > /# TableCol  3 Units unitless/
> > /# TableCol  4 ColHeader Volume_mm3/
> > /# TableCol  4 FieldName Volume/
> > /# TableCol  4 Units mm^3/
> > /# TableCol  5 ColHeader Mean /
> > /# TableCol  5 FieldName Intensity Mean/
> > /# TableCol  5 Units unknown/
> > /# TableCol  6 ColHeader StdDev/
> > /# TableCol  6 FieldName Itensity StdDev/
> > /# TableCol  6 Units unknown/
> > /# TableCol  7 ColHeader Min/
> > /# TableCol  7 FieldName Intensity Min/
> > /# TableCol  7 Units unknown/
> > /# TableCol  8 ColHeader Max/
> > /# TableCol  8 FieldName Intensity Max/
> > /# TableCol  8 Units unknown/
> > /# TableCol  9 ColHeader Range/
> > /# TableCol  9 FieldName Intensity Range/
> > /# TableCol  9 Units unknown/
> > /# NRows 1 /
> > /# NTableCols 9 /
> > /# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev
> > Min Max Range /
> > /  1   1 1151011510.0  Seg0001 7.6819  1.4396
> > 4.486210.9042 6.4180 /
> >
> > As my inputs are all surface data could I consider that NVoxels is
> > equal to NVertices and Volume_mm3 is equal to SurfaceArea_mm2 ?
> >
> > Best regards,
> > Matthieu
> >
> >> Le 10 nov. 2016 à 23:18, Matthieu Vanhoutte
> >>  
>  >> a
> >> écrit :
> >>
> >> Thank you Douglas !
> >>
> >>
> >> Le 10 nov. 2016 7:21 PM, "Douglas N Greve"
> 
> >>  >> a écrit :
> >>
> >> You need to weight by the number of vertices
> >>
> >> n = [27805 2321 552];
> >>   m = [8.8194 10.3661 10.3365];
> >> sum(n.*m)/sum(n)
> >>
> >> ans =
> >>
> >>  8.9637
> >>
> >>
> >> On 11/10/2016 06:44 AM, Matthieu Vanhoutte wrote:
> >> > Dear Freesurfer's experts,
> >> >
> >> > Could anyone please explain me the difference I got with
> >> command line
> >> > in below mail ?
> >> >
> >> > Best regards,
> >> > Matthieu
> >> >
> >> > 2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte
> >> >  
> >>  >
> >>  
> >>   >> >
> >> > Dear experts,
> >> >
> >> > I am in trouble with 

Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple input scans

[Krieger, Donald N.]

Now I don't understand.

Here's the situation:
Someone has given me a bunch of MEG's with freesurfer runs which were run using 
both a T1 and a T2 scan with -T2pial .
 Mri_info --tkr2scanner gives the same transform for aparac+aseg.mgz, T1.mgz, 
and T2.mgz  .
I will be coregistering the MEG which comes with each T1/T2 pair .
Since I'm getting the same transform from all the .mgz's, I speculated that 
freesurfer transformed both scans to tkr coordinates, did its thing, and then 
picked the T1 to provide the tkr2scanner transform.  
???

Don


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Friday, November 11, 2016 4:35 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple 
> input
> scans
> 
> If the head has not moved, then they will share a scanner RAS, ie,  a given
> scanner RAS will be at the same place in the head in the two scans, though 
> they
> will map to different col,row,slice in their respective volumes. If the head 
> has
> moved, then you will need to perform a registration to get them aligned.
> 
> 
> On 11/11/2016 04:17 PM, Krieger, Donald N. wrote:
> > Thanks for getting back, Doug.
> > I understand - but if there are two scans, aren't there two scanner RAS's 
> > since
> the head presumably moved at least a little from one to the other or the scans
> could have been done on different scanners?
> >
> > Don
> >
> > 
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> > [gr...@nmr.mgh.harvard.edu]
> > Sent: Friday, November 11, 2016 3:22 PM
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] mri_info --tkr2scanner result for run with
> > multiple input scans
> >
> > -tkr2scanner gives the transform that takes "tkregister RAS" and
> > converts it to scanner RAS. "tkregisterRAS" is the RAS system used by
> > surfaces (it, a vertex xyz is in tkregisterRAS). See
> > http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
> >
> >
> >
> > On 11/10/2016 09:33 PM, Krieger, Donald N. wrote:
> >> If I run recon-all with both a T1 and a T2 scan and switch t2pial,
> >> does mri_info -tkr2scanner give me the transform to the T1 scanner
> >> frame of reference?
> >>
> >> And if I run recon-all with many T1's , what does mri_info
> >> -tkr2scanner give me then?
> >>
> >> Thanks - Don
> >>
> >>
> >>
> >> ___
> >> 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
> >
> >
> 
> --
> 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

___
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Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

[Douglas N Greve]

If you want to do it on fsaverage, then

mris_segstats --i $SUBJECTS/fsaverage/surf/lh.white.avg.area.mgh --seg 
lh.sign_clust.bin.mgh
--excludeid 0 --sum lh.bin.area.sum --accumulate




On 11/11/2016 04:48 PM, Matthieu Vanhoutte wrote:
>
> Dear Douglas,
>
> Yes I would like to in order to compute mean of some means. Maybe not 
> if it is equivalent to number of vertices (are vertices distributed 
> equaly distant on the cortical surface ?)
>
> In case I need surface area, do I have to convert overlay to 
> annotation file to be used with mri_segstats ?
>
> Best regards,
> Matthieu
>
>
> Le 11 nov. 2016 9:21 PM, "Douglas N Greve"  > a écrit :
>
> NVox is the number of vertices. The Volume_mm3 is not meaningful.
> Do you
> want area?
>
>
> On 11/11/2016 04:53 AM, Matthieu Vanhoutte wrote:
> > Dear Douglas,
> >
> > I come back to you concerning stats made from binary .mgh
> surface data
> > file:
> >
> > mri_segstats --i lh.fsaverage.sm10.mgh --seg lh.sign_clust.bin.mgh
> > --excludeid 0 --sum lh.bin.sum --avgwf lh.wav.bin.txt
> >
> > In the output file « lh.bin.sum » all is considered as volume
> > input/output as you could see below:
> >
> > /# InVolFileTimeStamp  2016/04/28 09:46:19 /
> > /# InVolFrame 0 /
> > /# ExcludeSegId 0 /
> > /# Only reporting non-empty segmentations/
> > /# VoxelVolume_mm3 1 /
> > /# TableCol  1 ColHeader Index /
> > /# TableCol  1 FieldName Index /
> > /# TableCol  1 Units NA /
> > /# TableCol  2 ColHeader SegId /
> > /# TableCol  2 FieldName Segmentation Id/
> > /# TableCol  2 Units NA/
> > /# TableCol  3 ColHeader NVoxels /
> > /# TableCol  3 FieldName Number of Voxels/
> > /# TableCol  3 Units unitless/
> > /# TableCol  4 ColHeader Volume_mm3/
> > /# TableCol  4 FieldName Volume/
> > /# TableCol  4 Units mm^3/
> > /# TableCol  5 ColHeader Mean /
> > /# TableCol  5 FieldName Intensity Mean/
> > /# TableCol  5 Units unknown/
> > /# TableCol  6 ColHeader StdDev/
> > /# TableCol  6 FieldName Itensity StdDev/
> > /# TableCol  6 Units unknown/
> > /# TableCol  7 ColHeader Min/
> > /# TableCol  7 FieldName Intensity Min/
> > /# TableCol  7 Units unknown/
> > /# TableCol  8 ColHeader Max/
> > /# TableCol  8 FieldName Intensity Max/
> > /# TableCol  8 Units unknown/
> > /# TableCol  9 ColHeader Range/
> > /# TableCol  9 FieldName Intensity Range/
> > /# TableCol  9 Units unknown/
> > /# NRows 1 /
> > /# NTableCols 9 /
> > /# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev
> > Min Max Range /
> > /  1   1 1151011510.0  Seg0001 7.6819  1.4396
> > 4.486210.9042 6.4180 /
> >
> > As my inputs are all surface data could I consider that NVoxels is
> > equal to NVertices and Volume_mm3 is equal to SurfaceArea_mm2 ?
> >
> > Best regards,
> > Matthieu
> >
> >> Le 10 nov. 2016 à 23:18, Matthieu Vanhoutte
> >>  
>  >> a
> >> écrit :
> >>
> >> Thank you Douglas !
> >>
> >>
> >> Le 10 nov. 2016 7:21 PM, "Douglas N Greve"
> 
> >>  >> a écrit :
> >>
> >> You need to weight by the number of vertices
> >>
> >> n = [27805 2321 552];
> >>   m = [8.8194 10.3661 10.3365];
> >> sum(n.*m)/sum(n)
> >>
> >> ans =
> >>
> >>  8.9637
> >>
> >>
> >> On 11/10/2016 06:44 AM, Matthieu Vanhoutte wrote:
> >> > Dear Freesurfer's experts,
> >> >
> >> > Could anyone please explain me the difference I got with
> >> command line
> >> > in below mail ?
> >> >
> >> > Best regards,
> >> > Matthieu
> >> >
> >> > 2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte
> >> >  
> >>  >
> >>  
> >>   >> >
> >> > Dear experts,
> >> >
> >> > I am in trouble with two ways of computing mean
> intensity with
> >> > mri_segstats.
> >> >
> >> > First I have used on .annot files with three
> different labels
> >> > inside (SegId 1 to 3) :
> >> >
> >> >

Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

[Matthieu Vanhoutte]

Dear Douglas,

Yes I would like to in order to compute mean of some means. Maybe not if it
is equivalent to number of vertices (are vertices distributed equaly
distant on the cortical surface ?)

In case I need surface area, do I have to convert overlay to annotation
file to be used with mri_segstats ?

Best regards,
Matthieu

Le 11 nov. 2016 9:21 PM, "Douglas N Greve"  a
écrit :

> NVox is the number of vertices. The Volume_mm3 is not meaningful. Do you
> want area?
>
>
> On 11/11/2016 04:53 AM, Matthieu Vanhoutte wrote:
> > Dear Douglas,
> >
> > I come back to you concerning stats made from binary .mgh surface data
> > file:
> >
> > mri_segstats --i lh.fsaverage.sm10.mgh --seg lh.sign_clust.bin.mgh
> > --excludeid 0 --sum lh.bin.sum --avgwf lh.wav.bin.txt
> >
> > In the output file « lh.bin.sum » all is considered as volume
> > input/output as you could see below:
> >
> > /# InVolFileTimeStamp  2016/04/28 09:46:19 /
> > /# InVolFrame 0 /
> > /# ExcludeSegId 0 /
> > /# Only reporting non-empty segmentations/
> > /# VoxelVolume_mm3 1 /
> > /# TableCol  1 ColHeader Index /
> > /# TableCol  1 FieldName Index /
> > /# TableCol  1 Units NA /
> > /# TableCol  2 ColHeader SegId /
> > /# TableCol  2 FieldName Segmentation Id/
> > /# TableCol  2 Units NA/
> > /# TableCol  3 ColHeader NVoxels /
> > /# TableCol  3 FieldName Number of Voxels/
> > /# TableCol  3 Units unitless/
> > /# TableCol  4 ColHeader Volume_mm3/
> > /# TableCol  4 FieldName Volume/
> > /# TableCol  4 Units mm^3/
> > /# TableCol  5 ColHeader Mean /
> > /# TableCol  5 FieldName Intensity Mean/
> > /# TableCol  5 Units unknown/
> > /# TableCol  6 ColHeader StdDev/
> > /# TableCol  6 FieldName Itensity StdDev/
> > /# TableCol  6 Units unknown/
> > /# TableCol  7 ColHeader Min/
> > /# TableCol  7 FieldName Intensity Min/
> > /# TableCol  7 Units unknown/
> > /# TableCol  8 ColHeader Max/
> > /# TableCol  8 FieldName Intensity Max/
> > /# TableCol  8 Units unknown/
> > /# TableCol  9 ColHeader Range/
> > /# TableCol  9 FieldName Intensity Range/
> > /# TableCol  9 Units unknown/
> > /# NRows 1 /
> > /# NTableCols 9 /
> > /# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev
> > Min Max Range /
> > /  1   1 1151011510.0  Seg0001 7.6819 1.4396
> > 4.486210.9042 6.4180 /
> >
> > As my inputs are all surface data could I consider that NVoxels is
> > equal to NVertices and Volume_mm3 is equal to SurfaceArea_mm2 ?
> >
> > Best regards,
> > Matthieu
> >
> >> Le 10 nov. 2016 à 23:18, Matthieu Vanhoutte
> >> > a
> >> écrit :
> >>
> >> Thank you Douglas !
> >>
> >>
> >> Le 10 nov. 2016 7:21 PM, "Douglas N Greve"  >> > a écrit :
> >>
> >> You need to weight by the number of vertices
> >>
> >> n = [27805 2321 552];
> >>   m = [8.8194 10.3661 10.3365];
> >> sum(n.*m)/sum(n)
> >>
> >> ans =
> >>
> >>  8.9637
> >>
> >>
> >> On 11/10/2016 06:44 AM, Matthieu Vanhoutte wrote:
> >> > Dear Freesurfer's experts,
> >> >
> >> > Could anyone please explain me the difference I got with
> >> command line
> >> > in below mail ?
> >> >
> >> > Best regards,
> >> > Matthieu
> >> >
> >> > 2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte
> >> >  >> 
> >>  >> >>:
> >> >
> >> > Dear experts,
> >> >
> >> > I am in trouble with two ways of computing mean intensity with
> >> > mri_segstats.
> >> >
> >> > First I have used on .annot files with three different labels
> >> > inside (SegId 1 to 3) :
> >> >
> >> > /mri_segstats --annot fsaverage lh
> cache.th23.pos.sig.ocn.annot
> >> > --i lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum/
> >> > /
> >> > /
> >> > which give me those results:
> >> > # ColHeaders  Index SegId NVertices Area_mm2 StructName Mean
> >> > StdDev Min Max Range
> >> > 1   1 2780514182.6  cluster-001 8.8194 1.4351
> >> > 6.210514.2947 8.0842
> >> > 2   2  2321 1047.3  cluster-002  10.3661 1.0848
> >> > 8.837512.9317 4.0942
> >> > 3   3   552  313.1  cluster3 10.3365 0.4711
> >> > 9.371911.8694 2.4975
> >> >
> >> > Second I have created on .label files containing the three
> >> > segmented labels (SegId 1 to 3) and used this label with
> >> mri_segstats:
> >> >
> >> > /mri_segstats --slabel fsaverage lh
> >> > lh.th23.cluster.thresh1.3.label --i lh.PET.fsaverage.sm10.mgh
> >> > --excludeid 0 --sum lh.pet.label.sum /
> >> > /
> >> > /
> >> > 

Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple input scans

[Douglas N Greve]

If the head has not moved, then they will share a scanner RAS, ie,  a 
given scanner RAS will be at the same place in the head in the two 
scans, though they will map to different col,row,slice in their 
respective volumes. If the head has moved, then you will need to perform 
a registration to get them aligned.


On 11/11/2016 04:17 PM, Krieger, Donald N. wrote:
> Thanks for getting back, Doug.
> I understand - but if there are two scans, aren't there two scanner RAS's 
> since the head presumably moved at least a little from one to the other or 
> the scans could have been done on different scanners?
>
> Don
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, November 11, 2016 3:22 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple 
> input scans
>
> -tkr2scanner gives the transform that takes "tkregister RAS" and
> converts it to scanner RAS. "tkregisterRAS" is the RAS system used by
> surfaces (it, a vertex xyz is in tkregisterRAS). See
> http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
>
>
>
> On 11/10/2016 09:33 PM, Krieger, Donald N. wrote:
>> If I run recon-all with both a T1 and a T2 scan and switch t2pial,
>> does mri_info –tkr2scanner give me the transform to the T1 scanner
>> frame of reference?
>>
>> And if I run recon-all with many T1’s , what does mri_info
>> –tkr2scanner give me then?
>>
>> Thanks - Don
>>
>>
>>
>> ___
>> 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
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>
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>
>
> 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 
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> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
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>

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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple input scans

[Krieger, Donald N.]

Thanks for getting back, Doug.
I understand - but if there are two scans, aren't there two scanner RAS's since 
the head presumably moved at least a little from one to the other or the scans 
could have been done on different scanners?

Don


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Friday, November 11, 2016 3:22 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple 
input scans

-tkr2scanner gives the transform that takes "tkregister RAS" and
converts it to scanner RAS. "tkregisterRAS" is the RAS system used by
surfaces (it, a vertex xyz is in tkregisterRAS). See
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems



On 11/10/2016 09:33 PM, Krieger, Donald N. wrote:
>
> If I run recon-all with both a T1 and a T2 scan and switch t2pial,
> does mri_info –tkr2scanner give me the transform to the T1 scanner
> frame of reference?
>
> And if I run recon-all with many T1’s , what does mri_info
> –tkr2scanner give me then?
>
> Thanks - Don
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
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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
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Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

[Douglas N Greve]

NVox is the number of vertices. The Volume_mm3 is not meaningful. Do you 
want area?


On 11/11/2016 04:53 AM, Matthieu Vanhoutte wrote:
> Dear Douglas,
>
> I come back to you concerning stats made from binary .mgh surface data 
> file:
>
> mri_segstats --i lh.fsaverage.sm10.mgh --seg lh.sign_clust.bin.mgh 
> --excludeid 0 --sum lh.bin.sum --avgwf lh.wav.bin.txt
>
> In the output file « lh.bin.sum » all is considered as volume 
> input/output as you could see below:
>
> /# InVolFileTimeStamp  2016/04/28 09:46:19 /
> /# InVolFrame 0 /
> /# ExcludeSegId 0 /
> /# Only reporting non-empty segmentations/
> /# VoxelVolume_mm3 1 /
> /# TableCol  1 ColHeader Index /
> /# TableCol  1 FieldName Index /
> /# TableCol  1 Units NA /
> /# TableCol  2 ColHeader SegId /
> /# TableCol  2 FieldName Segmentation Id/
> /# TableCol  2 Units NA/
> /# TableCol  3 ColHeader NVoxels /
> /# TableCol  3 FieldName Number of Voxels/
> /# TableCol  3 Units unitless/
> /# TableCol  4 ColHeader Volume_mm3/
> /# TableCol  4 FieldName Volume/
> /# TableCol  4 Units mm^3/
> /# TableCol  5 ColHeader Mean /
> /# TableCol  5 FieldName Intensity Mean/
> /# TableCol  5 Units unknown/
> /# TableCol  6 ColHeader StdDev/
> /# TableCol  6 FieldName Itensity StdDev/
> /# TableCol  6 Units unknown/
> /# TableCol  7 ColHeader Min/
> /# TableCol  7 FieldName Intensity Min/
> /# TableCol  7 Units unknown/
> /# TableCol  8 ColHeader Max/
> /# TableCol  8 FieldName Intensity Max/
> /# TableCol  8 Units unknown/
> /# TableCol  9 ColHeader Range/
> /# TableCol  9 FieldName Intensity Range/
> /# TableCol  9 Units unknown/
> /# NRows 1 /
> /# NTableCols 9 /
> /# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev 
> Min Max Range /
> /  1   1 1151011510.0  Seg0001 7.6819 1.4396 
> 4.486210.9042 6.4180 /
>
> As my inputs are all surface data could I consider that NVoxels is 
> equal to NVertices and Volume_mm3 is equal to SurfaceArea_mm2 ?
>
> Best regards,
> Matthieu
>
>> Le 10 nov. 2016 à 23:18, Matthieu Vanhoutte 
>> > a 
>> écrit :
>>
>> Thank you Douglas !
>>
>>
>> Le 10 nov. 2016 7:21 PM, "Douglas N Greve" > > a écrit :
>>
>> You need to weight by the number of vertices
>>
>> n = [27805 2321 552];
>>   m = [8.8194 10.3661 10.3365];
>> sum(n.*m)/sum(n)
>>
>> ans =
>>
>>  8.9637
>>
>>
>> On 11/10/2016 06:44 AM, Matthieu Vanhoutte wrote:
>> > Dear Freesurfer's experts,
>> >
>> > Could anyone please explain me the difference I got with
>> command line
>> > in below mail ?
>> >
>> > Best regards,
>> > Matthieu
>> >
>> > 2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte
>> > > 
>> > >>:
>> >
>> > Dear experts,
>> >
>> > I am in trouble with two ways of computing mean intensity with
>> > mri_segstats.
>> >
>> > First I have used on .annot files with three different labels
>> > inside (SegId 1 to 3) :
>> >
>> > /mri_segstats --annot fsaverage lh cache.th23.pos.sig.ocn.annot
>> > --i lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum/
>> > /
>> > /
>> > which give me those results:
>> > # ColHeaders  Index SegId NVertices Area_mm2 StructName Mean
>> > StdDev Min Max Range
>> > 1   1 2780514182.6  cluster-001 8.8194 1.4351
>> > 6.210514.2947 8.0842
>> > 2   2  2321 1047.3  cluster-002  10.3661 1.0848
>> > 8.837512.9317 4.0942
>> > 3   3   552  313.1  cluster3 10.3365 0.4711
>> > 9.371911.8694 2.4975
>> >
>> > Second I have created on .label files containing the three
>> > segmented labels (SegId 1 to 3) and used this label with
>> mri_segstats:
>> >
>> > /mri_segstats --slabel fsaverage lh
>> > lh.th23.cluster.thresh1.3.label --i lh.PET.fsaverage.sm10.mgh
>> > --excludeid 0 --sum lh.pet.label.sum /
>> > /
>> > /
>> > which give me those results:/
>> > /
>> > /# ColHeaders  Index SegId NVertices Area_mm2 StructName Mean
>> > StdDev Min Max Range /
>> > /  1   1 30678  15542.9  Seg0001 8.96371.4701 6.2105
>> >  14.2947 8.0842 /
>> > /
>> > /
>> > I verified if I obtained the same results with the two ways
>> > (.annot or .label) and everything is fine comparing NVertices,
>> > Area_mm2 but Mean in first way gives me
>> (8.8194+10.3661+10.3365)/3
>> > = 9.84066 and with .label file Mean = 8.9637.
>> >
>> > Did I have miss anything and how is computed 

Re: [Freesurfer] mri_info --tkr2scanner result for run with multiple input scans

[Douglas N Greve]

-tkr2scanner gives the transform that takes "tkregister RAS" and 
converts it to scanner RAS. "tkregisterRAS" is the RAS system used by 
surfaces (it, a vertex xyz is in tkregisterRAS). See 
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems



On 11/10/2016 09:33 PM, Krieger, Donald N. wrote:
>
> If I run recon-all with both a T1 and a T2 scan and switch t2pial, 
> does mri_info –tkr2scanner give me the transform to the T1 scanner 
> frame of reference?
>
> And if I run recon-all with many T1’s , what does mri_info 
> –tkr2scanner give me then?
>
> Thanks - Don
>
>
>
> ___
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-- 
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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
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Re: [Freesurfer] recon all

[Douglas N Greve]

This can also happen if the head is oriented in a strange way. This can 
happen with older patients that tend to tilt their head back.


On 11/10/2016 08:27 PM, Bruce Fischl wrote:
> Hi John
>
> it means that the talairach transform that was computed was extremely 
> unlikely and deemed to be probably incorrect. Frequently this happens 
> if you start with images (like analyze) that don't contain accurate 
> direction cosine information. You can check this by bringing one of 
> the volumes in freeview and checking to make sure that the anatomical 
> directions we show
> (e.g. anterior/posterior) correspond to the true anatomy. Sometimes 
> abnormal anatomiies like huge ventricles can also make it fail, but 
> you need to figure out which one it is before deciding what to do
>
> cheers
> Bruce
>
>
> On Fri, 11 Nov 2016, John Anderson wrote:
>
>> Dear Freesurfer experts,
>> I ran the following command on a T1 image
>> recon-all -subjid 089 -all -qcache
>>
>> and I got the following error message:
>>
>> talairach_afd -T 0.005 -xfm transforms/talairach.xfm
>>
>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
>> ***FAILED*** (p=0.0344, pval=0.0034 < threshold=0.0050)
>>
>>
>> I highly appreciate an explanation for the meaning of this error and 
>> how to
>> fix it.
>>
>>
>> Best
>> John
>>
>>
>
>
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Re: [Freesurfer] CVS repository

[zkaufman]

This page should be more helpful for you.

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

-Zeke

> I am trying to checkout the development version of Freesurfer from the CVS
> repository.  I need to build against VTK 7.1 instead of 5.6 for freeview
> and am using these instructions:
> https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS
>
> Using this command:
>
>  cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot
> checkout -P dev
>
>
> Results in the following error:
>
>
> cvs server: cannot find module `dev' - ignored
>
> Can you tell me the correct module name?
>
>
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Re: [Freesurfer] differences between OS recon all output, longitudinal data

[zkaufman]

> Hi
>
> I am using recon-all in some longitudinal data on a ubuntu 16.04, and
> using
> the development version of freesurfer as I was told here, because the
> other
> current version doesnt work on ubuntu 16.04.
>
> The problem is that the first scans were probablly processed using
> virtualbox in a windows and an older version of freesurfer.
>
>
> i think I already know the answer, that I can't do this if I dont want to
> bias my results. Can I?

Yup. You know the answer ;) However, I did discover a way to make
freesurfer 5.3 work on Ubuntu 16 by doing the following steps to install
an older version of perl :

  1) install perlbrew:

$> sudo apt-get install perlbrew

  2) use perlbrew to install perl version 5.20.3:

$> perlbrew install perl-5.20.3

  3) You must change the '/bin/perl' file to a link which points to the
version of perl installed by perlbrew. (This technique is not the
standard practice but it is the only way to get the mni tools to use the
older version of perl):

$> cd /bin
$> sudo mv perl perl.orig (can always set back later)
$> ln -s ~/perl5/perlbrew/perls/perl-5.20.3/bin/perl


>
> But I'm using a better computer now and I use the one with windows for
> other analyses, so I wanted to know if I could install Virtual box on my
> ubuntu 16.04 computer, and install the same version of linux used to
> process the first measure. Should I also need to use the same version of
> freesurfer?


You could do that, but The Virtual Box version is not really good for
processing a large number of subjects because of the limited amount of
disk space on the virtual image. Its really meant more as a teaching tool
for users with Windows machines.

>
> f the computer's specs are dfferent, does it matter? And if I assign
> different cpu and ram on my virtual machine?

Different specs are fine. Its the OS, OS version,  and version of
freesurfer that should stay the same.


>
> Thank you!
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Re: [Freesurfer] AAL atlas

[Douglas N Greve]

Yes, mri_label2vol is the right command for this


On 11/11/2016 12:20 PM, stella maris sanchez wrote:
> Hi Doug, thanks for your response.
>
> I have one question more. I was reading the mail archive and I found a 
> few messages that talk about the mri_label2vol, vol2surf and surf2surf 
> commands. Specially the first one (mri_label2vol) the user said that 
> with it he moved the AAL to the subject's space. Do you think doing it 
> can help me? I'm not sure about the inputs of the command.
> Stella
>
>
> -- 
> Sánchez, Stella M.
>
>
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Re: [Freesurfer] FSL View in the virtual box version?

[Bruce Fischl]

Hi Jeffrey

I think this question is one for the FSL list, not for us.

cheers
Bruce
On Fri, 11 Nov 
2016, Jeffrey Crawford wrote:




Hello there!

 

I currently use the virtualbox version of freesurfer on my windows and the
CentOS 4 (32b) version on a linux computer. I noticed today that the Virtual
box version does not seem to have fsl view.

 

I found this link to a blog where this person has a virtual box that
contained fslview, but I think his methods and version are different from
the typical installation procedures.

 

http://kylemathewson.com/cnl-virtualbox-setup/

 

I was just wondering if it is possible to use fslview on the virtual box
version or not and how I might go about obtaining that capability?


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[Freesurfer] FSL View in the virtual box version?

[Jeffrey Crawford]

Hello there!

I currently use the virtualbox version of freesurfer on my windows and the 
CentOS 4 (32b) version on a linux computer. I noticed today that the Virtual 
box version does not seem to have fsl view.

I found this link to a blog where this person has a virtual box that contained 
fslview, but I think his methods and version are different from the typical 
installation procedures.

http://kylemathewson.com/cnl-virtualbox-setup/

I was just wondering if it is possible to use fslview on the virtual box 
version or not and how I might go about obtaining that capability?
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Re: [Freesurfer] AAL atlas

[stella maris sanchez]

Hi Doug, thanks for your response.

I have one question more. I was reading the mail archive and I found a few
messages that talk about the mri_label2vol, vol2surf and surf2surf
commands. Specially the first one (mri_label2vol) the user said that with
it he moved the AAL to the subject's space. Do you think doing it can help
me? I'm not sure about the inputs of the command.
Stella


-- 
Sánchez, Stella M.
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[Freesurfer] differences between OS recon all output, longitudinal data

[anonymous anonymous]

Hi

I am using recon-all in some longitudinal data on a ubuntu 16.04, and using
the development version of freesurfer as I was told here, because the other
current version doesnt work on ubuntu 16.04.

The problem is that the first scans were probablly processed using
virtualbox in a windows and an older version of freesurfer.


i think I already know the answer, that I can't do this if I dont want to
bias my results. Can I?

But I'm using a better computer now and I use the one with windows for
other analyses, so I wanted to know if I could install Virtual box on my
ubuntu 16.04 computer, and install the same version of linux used to
process the first measure. Should I also need to use the same version of
freesurfer?

f the computer's specs are dfferent, does it matter? And if I assign
different cpu and ram on my virtual machine?

Thank you!
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Re: [Freesurfer] Large Ventricles

[Bruce Fischl]

Hi Tamara

not really. The older versions didn't handle them that well, which I guess 
means you have to manually edit the asegs.


cheers
Bruce


On Fri, 11 Nov 2016, Tamara Tavares wrote:


Hello,

I have a participant who has very large ventricles and as a result, there
are substantial errors in the aseg output. Looking at the mailing list, I
see that the newest version of Freesurfer is suppose to be better at
handling large ventricles; however, I want to be consistent with the
Freesurfer version I have been using (version 5.1). Are there any other
recommendations with dealing with large ventricles? 

Thank you in advance for your help,
Tamara

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[Freesurfer] ERROR: make_roi_paths did not complete successfully!

[Hari Guragain]

Hi Freesurfer experts,

I was working on to conduct the local gyrification index analysis. I am
getting the following error message when I used the option -localGI in
recon-all.



Improper assignment with rectangular empty matrix.

Error in dsearchn (line 79)

[d(i),t(i)] = min(sum((x-yi).^2,2));

Error in mesh_vertex_nearest (line 29)

nearestIndex = dsearchn(vertices,points);

Error in reorganize_verticeslist (line 28)


[nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));



Error in make_roi_paths (line 93)

reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim,

verticeslist, step);

ERROR:  make_roi_paths did not complete successfully!



I have seen people have similar problem long time ago (
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg33701.html).

I also tried to check the SearchProjectionOnPial.m file and it looks same
as what was attached in the email.


Can anyone help on this?

I will really appreciate.

Thank you,


Hari
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[Freesurfer] Large Ventricles

[Tamara Tavares]

Hello,

I have a participant who has very large ventricles and as a result, there
are substantial errors in the aseg output. Looking at the mailing list, I
see that the newest version of Freesurfer is suppose to be better at
handling large ventricles; however, I want to be consistent with the
Freesurfer version I have been using (version 5.1). Are there any other
recommendations with dealing with large ventricles?

Thank you in advance for your help,
Tamara
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Re: [Freesurfer] Mean intensity with mri_segstats : different results with .annot or .label

[Matthieu Vanhoutte]

Dear Douglas,

I come back to you concerning stats made from binary .mgh surface data file:

mri_segstats --i lh.fsaverage.sm10.mgh --seg lh.sign_clust.bin.mgh --excludeid 
0 --sum lh.bin.sum --avgwf lh.wav.bin.txt 

In the output file « lh.bin.sum » all is considered as volume input/output as 
you could see below:

# InVolFileTimeStamp  2016/04/28 09:46:19 
# InVolFrame 0 
# ExcludeSegId 0 
# Only reporting non-empty segmentations
# VoxelVolume_mm3 1 
# TableCol  1 ColHeader Index 
# TableCol  1 FieldName Index 
# TableCol  1 Units NA 
# TableCol  2 ColHeader SegId 
# TableCol  2 FieldName Segmentation Id
# TableCol  2 Units NA
# TableCol  3 ColHeader NVoxels 
# TableCol  3 FieldName Number of Voxels
# TableCol  3 Units unitless
# TableCol  4 ColHeader Volume_mm3
# TableCol  4 FieldName Volume
# TableCol  4 Units mm^3
# TableCol  5 ColHeader Mean 
# TableCol  5 FieldName Intensity Mean
# TableCol  5 Units unknown
# TableCol  6 ColHeader StdDev
# TableCol  6 FieldName Itensity StdDev
# TableCol  6 Units unknown
# TableCol  7 ColHeader Min
# TableCol  7 FieldName Intensity Min
# TableCol  7 Units unknown
# TableCol  8 ColHeader Max
# TableCol  8 FieldName Intensity Max
# TableCol  8 Units unknown
# TableCol  9 ColHeader Range
# TableCol  9 FieldName Intensity Range
# TableCol  9 Units unknown
# NRows 1 
# NTableCols 9 
# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max 
Range  
  1   1 1151011510.0  Seg0001 7.6819 1.4396 4.4862
10.9042 6.4180 

As my inputs are all surface data could I consider that NVoxels is equal to 
NVertices and Volume_mm3 is equal to SurfaceArea_mm2 ?

Best regards,
Matthieu

> Le 10 nov. 2016 à 23:18, Matthieu Vanhoutte  a 
> écrit :
> 
> Thank you Douglas !
> 
> 
> Le 10 nov. 2016 7:21 PM, "Douglas N Greve"  > a écrit :
> You need to weight by the number of vertices
> 
> n = [27805 2321 552];
>   m = [8.8194 10.3661 10.3365];
> sum(n.*m)/sum(n)
> 
> ans =
> 
>  8.9637
> 
> 
> On 11/10/2016 06:44 AM, Matthieu Vanhoutte wrote:
> > Dear Freesurfer's experts,
> >
> > Could anyone please explain me the difference I got with command line
> > in below mail ?
> >
> > Best regards,
> > Matthieu
> >
> > 2016-08-12 12:07 GMT+02:00 Matthieu Vanhoutte
> >  
> > >>:
> >
> > Dear experts,
> >
> > I am in trouble with two ways of computing mean intensity with
> > mri_segstats.
> >
> > First I have used on .annot files with three different labels
> > inside (SegId 1 to 3) :
> >
> > /mri_segstats --annot fsaverage lh cache.th23.pos.sig.ocn.annot
> > --i lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum/
> > /
> > /
> > which give me those results:
> > # ColHeaders  Index SegId NVertices Area_mm2 StructName Mean
> > StdDev Min Max Range
> > 1   1 2780514182.6  cluster-001  8.8194 1.4351
> > 6.210514.2947 8.0842
> > 2   2  2321 1047.3  cluster-002 10.3661 1.0848
> > 8.837512.9317 4.0942
> > 3   3   552  313.1  cluster3  10.3365 0.4711
> > 9.371911.8694 2.4975
> >
> > Second I have created on .label files containing the three
> > segmented labels (SegId 1 to 3) and used this label with mri_segstats:
> >
> > /mri_segstats --slabel fsaverage lh
> > lh.th23.cluster.thresh1.3.label --i lh.PET.fsaverage.sm10.mgh
> > --excludeid 0 --sum lh.pet.label.sum /
> > /
> > /
> > which give me those results:/
> > /
> > /# ColHeaders  Index SegId NVertices Area_mm2 StructName Mean
> > StdDev Min Max Range /
> > /  1   1 30678  15542.9  Seg0001 8.9637 1.4701 6.2105
> >  14.2947 8.0842 /
> > /
> > /
> > I verified if I obtained the same results with the two ways
> > (.annot or .label) and everything is fine comparing NVertices,
> > Area_mm2 but Mean in first way gives me (8.8194+10.3661+10.3365)/3
> > = 9.84066 and with .label file Mean = 8.9637.
> >
> > Did I have miss anything and how is computed mean intensity ?
> >
> > Many thanks in advance.
> >
> > Best regards,
> > Matthieu
> >
> >
> >
> >
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> > 
> 
> --
> 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: