Re: [Freesurfer] Freesurfer Digest, Vol 109, Issue 21

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Rotem Saar

24 Mar 2013 24 Mar '13

7:43 a.m.

Hi Doug,

Thanks for your answer. I changed the last step as u suggested, but I think I need to clarify my question: Indeed values of the CC looks OK, but don't u think other values, like the ventricles are too high ?

When I first run the script, I got all values and looked the the CC - it looked fine. Then, I wanted to validate with some other regions, just to show that I got the appropriate (low) FA values for regions I don't expect to see high values in - and things looked odd (too high).

I remember Bruce also writing me that the values seems a little high, but we didn't further discuss. I read the following this link: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalDtiIndividual

"The CC has an average FA of about 0.75, gyral parcellations are about 0.4, the left putamen is 0.27, and the ventricle is 0.2. This is as expected because the CC is highly directional with no crossing fibers so we would expect the CC to have the highest FA. The gyral white matter is also directional but has fibers crossing in them, so one expects the FA to be lower than CC. The gray matter (putamen) is still lower. The ventricle has no fibers, so we expect it to have the lowest FA".

All my values are above 0.4....

Additionally, if in the last step I'm writing --seg /usr/local/freesurfer/subjects/Rotem_try/mri/wmparc.mgz

why do I get 182 regions ? in my wmparc.stats I have only 70...

I'm probably doing something wrong, but I can't really point to the problem, thus asking for your help.

Attached is the table again,

Thanks Rotem

...

The values look about right in the table. Your pipeline looks ok, thought the last step uses fa_FOLDER-NAME.mask.nii instead of the output of mri_vol2vol (fa_FOLDER-NAME.nii). doug

On 03/17/2013 02:16 AM, Rotem Saar wrote:

...

Hi all,
I run into somthing that seems odd to me and wanted to consult -
I run the following script for getting the FA values from my DTI
scans:

1) dt_recon --i
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I00001.dcm --s
FOLDER-NAME --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec
2) tkregister2 --s fsaverage --surf white --reg
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg
--mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii
3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg wmparc.mgz
-reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat
-overlay /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii
-fthresh 0.2 -fmax 1
4) mri_vol2vol --mov
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ
/usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s
FOLDER-NAME --interp nearest --o
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii
--reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat
5) tkregister2 --mov
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii
--targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz
--reg
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg
6) mri_segstats --seg
/usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --i

/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii

...

--sum

/usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME

...

I got a table with all the FA values (see attached), for each
segment, but I suspect a problem: I think that the values are too
high (I set the threshold to 0.2-1), am I right ?
Can u guide me regarding what I can do to solve the problem ? in
addition I attached a figure of the corpus-callosum, in which I'm
interested - i't seems that the green area in not big enough, is
this fixable ?

Thanks !

Rotem

Attachments:

attachment.html (text/html — 4.8 KB)
all_stats_fa_Rotem_try.bin (application/octet-stream — 22.9 KB)

Show replies by date

Douglas N Greve

25 Mar 25 Mar

12:59 p.m.

New subject: Freesurfer Digest, Vol 109, Issue 21

Yes, .4 is probably too high. What is fa_FOLDER-NAME.mask.nii? In your code below, there is no indication of how it was generated.

There could be several things going on. One is that the registration is off. Have you check the reg? What is the first value of register.dat.mincost? The second thing is that it could be that the bvects/bvals. Finally, it could be your data that is off.

doug

On 03/24/2013 07:43 AM, Rotem Saar wrote:

...

Hi Doug,

Thanks for your answer. I changed the last step as u suggested, but I think I need to clarify my question: Indeed values of the CC looks OK, but don't u think other values, like the ventricles are too high ?

When I first run the script, I got all values and looked the the CC - it looked fine. Then, I wanted to validate with some other regions, just to show that I got the appropriate (low) FA values for regions I don't expect to see high values in - and things looked odd (too high).

I remember Bruce also writing me that the values seems a little high, but we didn't further discuss. I read the following this link: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalDtiIndividual

"The CC has an average FA of about 0.75, gyral parcellations are about 0.4, the left putamen is 0.27, and the ventricle is 0.2. This is as expected because the CC is highly directional with no crossing fibers so we would expect the CC to have the highest FA. The gyral white matter is also directional but has fibers crossing in them, so one expects the FA to be lower than CC. The gray matter (putamen) is still lower. The ventricle has no fibers, so we expect it to have the lowest FA".

All my values are above 0.4....

Additionally, if in the last step I'm writing --seg /usr/local/freesurfer/subjects/Rotem_try/mri/wmparc.mgz

why do I get 182 regions ? in my wmparc.stats I have only 70...

I'm probably doing something wrong, but I can't really point to the problem, thus asking for your help.

Attached is the table again,

Thanks Rotem
The values look about right in the table. Your pipeline looks ok,
thought the last step uses fa_FOLDER-NAME.mask.nii instead of the
output
of mri_vol2vol (fa_FOLDER-NAME.nii).
doug



On 03/17/2013 02:16 AM, Rotem Saar wrote:
>
>     Hi all,
>     I run into somthing that seems odd to me and wanted to consult -
>     I run the following script for getting the FA values from my DTI
>     scans:
>
>     1) dt_recon --i
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I00001.dcm --s
>     FOLDER-NAME --o
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec
>     2) tkregister2 --s fsaverage --surf white --reg
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg
>     --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii
>     3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg wmparc.mgz
>     -reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat
>     -overlay /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii
>     -fthresh 0.2 -fmax 1
>     4) mri_vol2vol --mov
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ
> /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s
>     FOLDER-NAME --interp nearest --o
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii
>     --reg
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat
>     5) tkregister2 --mov
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii
>     --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz
>     --reg
>
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg
>     6) mri_segstats --seg
> /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab
>     $FREESURFER_HOME/FreeSurferColorLUT.txt --i
>
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii
>     --sum
>
/usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME
>
>
>     I got a table with all the FA values (see attached), for each
>     segment, but I suspect a problem: I think that the values
are too
>     high (I set the threshold to 0.2-1), am I right ?
>     Can u guide me regarding what I can do to solve the problem ? in
>     addition I attached a figure of the corpus-callosum, in
which I'm
>     interested - i't seems that the green area in not big enough, is
>     this fixable ?
>
>     Thanks !
>
>     Rotem
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

Douglas N Greve

1:05 p.m.

New subject: Freesurfer Digest, Vol 109, Issue 21

ps. you are getting 182 segs because that's how many there are in wmparc; it includes cortical and subortical gray. You don't get that many in wmparc.stats because we only report WM structures. doug

On 03/25/2013 12:59 PM, Douglas N Greve wrote:

...

Yes, .4 is probably too high. What is fa_FOLDER-NAME.mask.nii? In your code below, there is no indication of how it was generated.

There could be several things going on. One is that the registration is off. Have you check the reg? What is the first value of register.dat.mincost? The second thing is that it could be that the bvects/bvals. Finally, it could be your data that is off.

doug

On 03/24/2013 07:43 AM, Rotem Saar wrote:

...
Hi Doug,

Thanks for your answer. I changed the last step as u suggested, but I think I need to clarify my question: Indeed values of the CC looks OK, but don't u think other values, like the ventricles are too high ?

When I first run the script, I got all values and looked the the CC - it looked fine. Then, I wanted to validate with some other regions, just to show that I got the appropriate (low) FA values for regions I don't expect to see high values in - and things looked odd (too high).

I remember Bruce also writing me that the values seems a little high, but we didn't further discuss. I read the following this link: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalDtiIndividual

"The CC has an average FA of about 0.75, gyral parcellations are about 0.4, the left putamen is 0.27, and the ventricle is 0.2. This is as expected because the CC is highly directional with no crossing fibers so we would expect the CC to have the highest FA. The gyral white matter is also directional but has fibers crossing in them, so one expects the FA to be lower than CC. The gray matter (putamen) is still lower. The ventricle has no fibers, so we expect it to have the lowest FA".

All my values are above 0.4....

Additionally, if in the last step I'm writing --seg /usr/local/freesurfer/subjects/Rotem_try/mri/wmparc.mgz

why do I get 182 regions ? in my wmparc.stats I have only 70...

I'm probably doing something wrong, but I can't really point to the problem, thus asking for your help.

Attached is the table again,

Thanks Rotem
 The values look about right in the table. Your pipeline looks ok,
 thought the last step uses fa_FOLDER-NAME.mask.nii instead of the
 output
 of mri_vol2vol (fa_FOLDER-NAME.nii).
 doug



 On 03/17/2013 02:16 AM, Rotem Saar wrote:
 >
 >     Hi all,
 >     I run into somthing that seems odd to me and wanted to consult -
 >     I run the following script for getting the FA values from my DTI
 >     scans:
 >
 >     1) dt_recon --i
 > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I00001.dcm --s
 >     FOLDER-NAME --o
 /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b
 > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval
 > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec
 >     2) tkregister2 --s fsaverage --surf white --reg
 > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg
 >     --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii
 >     3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg wmparc.mgz
 >     -reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat
 >     -overlay /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii
 >     -fthresh 0.2 -fmax 1
 >     4) mri_vol2vol --mov
 > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ
 > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s
 >     FOLDER-NAME --interp nearest --o
 > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii
 >     --reg
 /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat
 >     5) tkregister2 --mov
 > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii
 >     --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz
 >     --reg
 >
 /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg
 >     6) mri_segstats --seg
 > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab
 >     $FREESURFER_HOME/FreeSurferColorLUT.txt --i
 >
 /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii
 >     --sum
 >
 /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME
 >
 >
 >     I got a table with all the FA values (see attached), for each
 >     segment, but I suspect a problem: I think that the values
 are too
 >     high (I set the threshold to 0.2-1), am I right ?
 >     Can u guide me regarding what I can do to solve the problem ? in
 >     addition I attached a figure of the corpus-callosum, in
 which I'm
 >     interested - i't seems that the green area in not big enough, is
 >     this fixable ?
 >
 >     Thanks !
 >
 >     Rotem
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Rotem Saar

7 Apr 7 Apr

6:48 a.m.

New subject: Fwd: Freesurfer Digest, Vol 109, Issue 21

Hi Doug,

All my values are above 0.4....

Additionally, if in the last step I'm writing --seg /usr/local/freesurfer/subjects/Rotem_try/mri/wmparc.mgz

why do I get 182 regions ? in my wmparc.stats I have only 70...

I'm probably doing something wrong, but I can't really point to the problem, thus asking for your help.

Attached is the table again,

Thanks Rotem

...

The values look about right in the table. Your pipeline looks ok, thought the last step uses fa_FOLDER-NAME.mask.nii instead of the output of mri_vol2vol (fa_FOLDER-NAME.nii). doug

On 03/17/2013 02:16 AM, Rotem Saar wrote:

...

Hi all,
I run into somthing that seems odd to me and wanted to consult -
I run the following script for getting the FA values from my DTI
scans:

1) dt_recon --i
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I00001.dcm --s
FOLDER-NAME --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec
2) tkregister2 --s fsaverage --surf white --reg
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg
--mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii
3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg wmparc.mgz
-reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat
-overlay /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii
-fthresh 0.2 -fmax 1
4) mri_vol2vol --mov
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ
/usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s
FOLDER-NAME --interp nearest --o
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii
--reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat
5) tkregister2 --mov
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii
--targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz
--reg
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg
6) mri_segstats --seg
/usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --i

/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii

...

--sum

/usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME

...

I got a table with all the FA values (see attached), for each
segment, but I suspect a problem: I think that the values are too
high (I set the threshold to 0.2-1), am I right ?
Can u guide me regarding what I can do to solve the problem ? in
addition I attached a figure of the corpus-callosum, in which I'm
interested - i't seems that the green area in not big enough, is
this fixable ?

Thanks !

Rotem

Douglas N Greve

8 Apr 8 Apr

10:26 a.m.

New subject: Fwd: Freesurfer Digest, Vol 109, Issue 21

On 04/07/2013 06:48 AM, Rotem Saar wrote:

...

Hi Doug,

Thanks for your answer. I changed the last step as u suggested, but I think I need to clarify my question: Indeed values of the CC looks OK, but don't u think other values, like the ventricles are too high ?

yes, the ventricles look too high

...

When I first run the script, I got all values and looked the the CC - it looked fine. Then, I wanted to validate with some other regions, just to show that I got the appropriate (low) FA values for regions I don't expect to see high values in - and things looked odd (too high).

I remember Bruce also writing me that the values seems a little high, but we didn't further discuss. I read the following this link: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalDtiIndividual

"The CC has an average FA of about 0.75, gyral parcellations are about 0.4, the left putamen is 0.27, and the ventricle is 0.2. This is as expected because the CC is highly directional with no crossing fibers so we would expect the CC to have the highest FA. The gyral white matter is also directional but has fibers crossing in them, so one expects the FA to be lower than CC. The gray matter (putamen) is still lower. The ventricle has no fibers, so we expect it to have the lowest FA".

All my values are above 0.4....

Additionally, if in the last step I'm writing --seg /usr/local/freesurfer/subjects/Rotem_try/mri/wmparc.mgz

why do I get 182 regions ? in my wmparc.stats I have only 70...

The wmparc includes all the subcortical and cortical regions too, but only the WM regions are reported in the wmparc.stats file. To only report the WM regions, add to mri_segstats --ctab $FREESURFER_HOME/WMParcStatsLUT.txt

...

I'm probably doing something wrong, but I can't really point to the problem, thus asking for your help.

I don't know either. If I had to guess, I'd say it is a registration problem. What is the first value in register.dat.mincost? doug

...

Attached is the table again,

Thanks Rotem

The values look about right in the table. Your pipeline looks ok,
thought the last step uses fa_FOLDER-NAME.mask.nii instead of the
output
of mri_vol2vol (fa_FOLDER-NAME.nii).
doug



On 03/17/2013 02:16 AM, Rotem Saar wrote:
>
>     Hi all,
>     I run into somthing that seems odd to me and wanted to consult -
>     I run the following script for getting the FA values from my DTI
>     scans:
>
>     1) dt_recon --i
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I00001.dcm --s
>     FOLDER-NAME --o
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec
>     2) tkregister2 --s fsaverage --surf white --reg
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg
>     --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii
>     3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg wmparc.mgz
>     -reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat
>     -overlay /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii
>     -fthresh 0.2 -fmax 1
>     4) mri_vol2vol --mov
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ
> /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s
>     FOLDER-NAME --interp nearest --o
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii
>     --reg
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat
>     5) tkregister2 --mov
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii
>     --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz
>     --reg
>
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg
>     6) mri_segstats --seg
> /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab
>     $FREESURFER_HOME/FreeSurferColorLUT.txt --i
>
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii
>     --sum
>
/usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME
>
>
>     I got a table with all the FA values (see attached), for each
>     segment, but I suspect a problem: I think that the values
are too
>     high (I set the threshold to 0.2-1), am I right ?
>     Can u guide me regarding what I can do to solve the problem ? in
>     addition I attached a figure of the corpus-callosum, in
which I'm
>     interested - i't seems that the green area in not big enough, is
>     this fixable ?
>
>     Thanks !
>
>     Rotem

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

Douglas N Greve

30 Apr 30 Apr

6:02 p.m.

New subject: Freesurfer Digest, Vol 109, Issue 21

Hi Rotem, I've looked at your data and I cannot find anything explicity wrong. The FA values are just really high. The only thing I can think is that your bvalues are not right or that there is something else wrong with the data. sorry! doug

On 03/24/2013 07:43 AM, Rotem Saar wrote:

...

Hi Doug,

Thanks for your answer. I changed the last step as u suggested, but I think I need to clarify my question: Indeed values of the CC looks OK, but don't u think other values, like the ventricles are too high ?

When I first run the script, I got all values and looked the the CC - it looked fine. Then, I wanted to validate with some other regions, just to show that I got the appropriate (low) FA values for regions I don't expect to see high values in - and things looked odd (too high).

I remember Bruce also writing me that the values seems a little high, but we didn't further discuss. I read the following this link: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalDtiIndividual

"The CC has an average FA of about 0.75, gyral parcellations are about 0.4, the left putamen is 0.27, and the ventricle is 0.2. This is as expected because the CC is highly directional with no crossing fibers so we would expect the CC to have the highest FA. The gyral white matter is also directional but has fibers crossing in them, so one expects the FA to be lower than CC. The gray matter (putamen) is still lower. The ventricle has no fibers, so we expect it to have the lowest FA".

All my values are above 0.4....

Additionally, if in the last step I'm writing --seg /usr/local/freesurfer/subjects/Rotem_try/mri/wmparc.mgz

why do I get 182 regions ? in my wmparc.stats I have only 70...

I'm probably doing something wrong, but I can't really point to the problem, thus asking for your help.

Attached is the table again,

Thanks Rotem
The values look about right in the table. Your pipeline looks ok,
thought the last step uses fa_FOLDER-NAME.mask.nii instead of the
output
of mri_vol2vol (fa_FOLDER-NAME.nii).
doug



On 03/17/2013 02:16 AM, Rotem Saar wrote:
>
>     Hi all,
>     I run into somthing that seems odd to me and wanted to consult -
>     I run the following script for getting the FA values from my DTI
>     scans:
>
>     1) dt_recon --i
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I00001.dcm --s
>     FOLDER-NAME --o
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec
>     2) tkregister2 --s fsaverage --surf white --reg
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg
>     --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii
>     3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg wmparc.mgz
>     -reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat
>     -overlay /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii
>     -fthresh 0.2 -fmax 1
>     4) mri_vol2vol --mov
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ
> /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s
>     FOLDER-NAME --interp nearest --o
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii
>     --reg
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat
>     5) tkregister2 --mov
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii
>     --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz
>     --reg
>
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg
>     6) mri_segstats --seg
> /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab
>     $FREESURFER_HOME/FreeSurferColorLUT.txt --i
>
/usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii
>     --sum
>
/usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME
>
>
>     I got a table with all the FA values (see attached), for each
>     segment, but I suspect a problem: I think that the values
are too
>     high (I set the threshold to 0.2-1), am I right ?
>     Can u guide me regarding what I can do to solve the problem ? in
>     addition I attached a figure of the corpus-callosum, in
which I'm
>     interested - i't seems that the green area in not big enough, is
>     this fixable ?
>
>     Thanks !
>
>     Rotem
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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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Douglas N Greve
Rotem Saar