Re: [Freesurfer] hello freesurfer developer~

[A-reum Min]

Hello bruce

I solve this problem(12.png)

Thank you

2015-07-27 13:03 GMT+09:00 dgw :

> Hi A-reum,
>
> I think you may be able to get a faster response if you include some
> details about your setup: I would start with the following:
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> and run bugr.
>
> hth
> D
>
> On 7/26/15 5:17 PM, A-reum Min wrote:
> > Hi, Bruce
> >
> > When i use a Qdec, this message(12.png) show up..
> > How can i solve this problem?
> >
> > 2015-07-23 22:57 GMT+09:00 Bruce Fischl  > >:
> >
> > 1. No, each subject has a different #. You can map to fsaverage
> > (this is what -qcache does if you specify it for recon-all), then
> > they will have the same #.
> >
> > 2. What result data do you mean?
> >
> > 3. Yes, although I'll leave the details to Doug (since I don't
> > remember how his cluster code works).
> >
> > 4. The significance doesn't depend on the cluster size unless you do
> > multiple comparison corrections (and even then only if you do them a
> > certain way)
> >
> > cheers
> > Bruce
> >
> >
> > On Thu, 23 Jul 2015, A-reum Min wrote:
> >
> > HELLO developer
> > I have some question to you..
> >
> > 1. Every patient is given to the same number of vertex?
> >
> > 2. When i use a Qdec, How can I get the subject result data?
> >
> > 3. Could i get the significant vertex’s number, extent of the
> > significant area and gray matter volume?
> >
> > 4. Is it significant blue color which how many connected
> > vertex?
> >
> >
> > 2015-05-29 2:03 GMT+09:00 A-reum Min  > >:
> >hello developer~
> > reconstruction is well done, so i'm doing on 'qdec' step..
> > Actually, i don't know how to treat the Design menu exactly..
> >
>  ---
> > Discrete(fixed factors) : diagnosis
> > continuous (covariate) : age , Left-Lateral-Ventricle
> >
>  ---
> > which one click before analyze?
> >
> > age range is 12years~24years/
> > all subjects are adolescent.
> > and no outlier in age range.. so.. age (continuous factor) does
> not
> > nasessart?
> >
> >
> > 2015-05-29 1:19 GMT+09:00 A-reum Min  > >:
> >hello developer~
> > reconstruction is well done, so i'm doing on 'qdec' step..
> > Actually, i don't know how to treat the Design menu exactly..
> >
>  ---
> > Discrete(fixed factors) : diagnosis
> > continuous (covariate) : age , Left-Lateral-Ventricle
> >
>  ---
> > which one click before analyze?
> >
> >
> >
> > 2015-04-05 21:41 GMT+09:00 Bruce Fischl
> > mailto:fis...@nmr.mgh.harvard.edu
> >>:
> >I'm glad it worked out
> >Bruce
> >On Sun, 5 Apr 2015, A-reum Min wrote:
> >
> >  Hello Bruce~
> >  You're right.. my PISA dicom file header
> >  is too short
> >  so, freesurfer didn't read it.
> >
> >  Therefore I use another subjects dicom
> >  file and then freesurfer read it!
> >
> >  thank you for u r adavice to me.
> >
> >  I really appreciate u
> >
> >  2015-04-05 7:08 GMT+09:00 Bruce Fischl
> >   > >:
> >Hi  A-reum
> >
> >the problem is that newer versions
> >  of scanner software compress
> >dicoms and the version of FS you
> >  have doesn't know how to read
> >it. So you need to decompress them
> >  before passing them to
> >recon-all
> >
> >cheers
> >Bruce
> >On Sun, 5 Apr 2015, A-reum Min
> >  wrote:
> >
> >  Hello developer~
> >
> >  Can you summarize what the
> >  problem is?
> >  ==>
> >  my problem is recon-all -i
> >  didn't working...
> >  so, if i type the recon-all
> >  -i~then show up theses
> >
> >
> > 
> >

Re: [Freesurfer] hello freesurfer developer~

[dgw]

Hi A-reum,

I think you may be able to get a faster response if you include some 
details about your setup: I would start with the following:

http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
and run bugr.

hth
D

On 7/26/15 5:17 PM, A-reum Min wrote:
> Hi, Bruce
>
> When i use a Qdec, this message(12.png) show up..
> How can i solve this problem?
>
> 2015-07-23 22:57 GMT+09:00 Bruce Fischl  >:
>
> 1. No, each subject has a different #. You can map to fsaverage
> (this is what -qcache does if you specify it for recon-all), then
> they will have the same #.
>
> 2. What result data do you mean?
>
> 3. Yes, although I'll leave the details to Doug (since I don't
> remember how his cluster code works).
>
> 4. The significance doesn't depend on the cluster size unless you do
> multiple comparison corrections (and even then only if you do them a
> certain way)
>
> cheers
> Bruce
>
>
> On Thu, 23 Jul 2015, A-reum Min wrote:
>
> HELLO developer
> I have some question to you..
>
> 1. Every patient is given to the same number of vertex?
>
> 2. When i use a Qdec, How can I get the subject result data?
>
> 3. Could i get the significant vertex’s number, extent of the
> significant area and gray matter volume?
>
> 4. Is it significant blue color which how many connected
> vertex?
>
>
> 2015-05-29 2:03 GMT+09:00 A-reum Min  >:
>hello developer~
> reconstruction is well done, so i'm doing on 'qdec' step..
> Actually, i don't know how to treat the Design menu exactly..
> 
> ---
> Discrete(fixed factors) : diagnosis
> continuous (covariate) : age , Left-Lateral-Ventricle
> 
> ---
> which one click before analyze?
>
> age range is 12years~24years/
> all subjects are adolescent.
> and no outlier in age range.. so.. age (continuous factor) does not
> nasessart?
>
>
> 2015-05-29 1:19 GMT+09:00 A-reum Min  >:
>hello developer~
> reconstruction is well done, so i'm doing on 'qdec' step..
> Actually, i don't know how to treat the Design menu exactly..
> 
> ---
> Discrete(fixed factors) : diagnosis
> continuous (covariate) : age , Left-Lateral-Ventricle
> 
> ---
> which one click before analyze?
>
>
>
> 2015-04-05 21:41 GMT+09:00 Bruce Fischl
> mailto:fis...@nmr.mgh.harvard.edu>>:
>I'm glad it worked out
>Bruce
>On Sun, 5 Apr 2015, A-reum Min wrote:
>
>  Hello Bruce~
>  You're right.. my PISA dicom file header
>  is too short
>  so, freesurfer didn't read it.
>
>  Therefore I use another subjects dicom
>  file and then freesurfer read it!
>
>  thank you for u r adavice to me.
>
>  I really appreciate u
>
>  2015-04-05 7:08 GMT+09:00 Bruce Fischl
>   >:
>Hi  A-reum
>
>the problem is that newer versions
>  of scanner software compress
>dicoms and the version of FS you
>  have doesn't know how to read
>it. So you need to decompress them
>  before passing them to
>recon-all
>
>cheers
>Bruce
>On Sun, 5 Apr 2015, A-reum Min
>  wrote:
>
>  Hello developer~
>
>  Can you summarize what the
>  problem is?
>  ==>
>  my problem is recon-all -i
>  didn't working...
>  so, if i type the recon-all
>  -i~then show up theses
>
>
> 
>  ERROR: 32512, see
>
>  /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out
>  for
>  more details
>  Linux localhost.localdomain
>  2.6.32-504.el6.x86_64 #1
> 

Re: [Freesurfer] hello freesurfer developer~

[Bruce Fischl]

Maybe Zeke or Ruopeng know?



> On Jul 26, 2015, at 5:17 PM, A-reum Min  wrote:
> 
> Hi, Bruce
> 
> When i use a Qdec, this message(12.png) show up..
> How can i solve this problem?
> 
> 2015-07-23 22:57 GMT+09:00 Bruce Fischl :
>> 1. No, each subject has a different #. You can map to fsaverage (this is 
>> what -qcache does if you specify it for recon-all), then they will have the 
>> same #.
>> 
>> 2. What result data do you mean?
>> 
>> 3. Yes, although I'll leave the details to Doug (since I don't remember how 
>> his cluster code works).
>> 
>> 4. The significance doesn't depend on the cluster size unless you do 
>> multiple comparison corrections (and even then only if you do them a certain 
>> way)
>> 
>> cheers
>> Bruce
>> 
>> 
>> On Thu, 23 Jul 2015, A-reum Min wrote:
>> 
>>> HELLO developer
>>> I have some question to you..
>>> 
>>> 1. Every patient is given to the same number of vertex?
>>> 
>>> 2. When i use a Qdec, How can I get the subject result data?
>>> 
>>> 3. Could i get the significant vertex’s number, extent of the
>>> significant area and gray matter volume?
>>> 
>>> 4. Is it significant blue color which how many connected vertex? 
>>> 
>>> 
>>> 2015-05-29 2:03 GMT+09:00 A-reum Min :
>>>   hello developer~
>>> reconstruction is well done, so i'm doing on 'qdec' step..
>>> Actually, i don't know how to treat the Design menu exactly..
>>> ---
>>> Discrete(fixed factors) : diagnosis
>>> continuous (covariate) : age , Left-Lateral-Ventricle
>>> ---
>>> which one click before analyze?
>>> 
>>> age range is 12years~24years/
>>> all subjects are adolescent.
>>> and no outlier in age range.. so.. age (continuous factor) does not
>>> nasessart?
>>> 
>>> 
>>> 2015-05-29 1:19 GMT+09:00 A-reum Min :
>>>   hello developer~
>>> reconstruction is well done, so i'm doing on 'qdec' step..
>>> Actually, i don't know how to treat the Design menu exactly..
>>> ---
>>> Discrete(fixed factors) : diagnosis
>>> continuous (covariate) : age , Left-Lateral-Ventricle
>>> ---
>>> which one click before analyze?
>>> 
>>> 
>>> 
>>> 2015-04-05 21:41 GMT+09:00 Bruce Fischl
>>> :
>>>   I'm glad it worked out
>>>   Bruce
>>>   On Sun, 5 Apr 2015, A-reum Min wrote:
>>> 
>>> Hello Bruce~
>>> You're right.. my PISA dicom file header
>>> is too short 
>>> so, freesurfer didn't read it.
>>> 
>>> Therefore I use another subjects dicom
>>> file and then freesurfer read it!
>>> 
>>> thank you for u r adavice to me.
>>> 
>>> I really appreciate u
>>> 
>>> 2015-04-05 7:08 GMT+09:00 Bruce Fischl
>>> :
>>>   Hi  A-reum
>>> 
>>>   the problem is that newer versions
>>> of scanner software compress
>>>   dicoms and the version of FS you
>>> have doesn't know how to read
>>>   it. So you need to decompress them
>>> before passing them to
>>>   recon-all
>>> 
>>>   cheers
>>>   Bruce
>>>   On Sun, 5 Apr 2015, A-reum Min
>>> wrote:
>>> 
>>> Hello developer~
>>>  
>>> Can you summarize what the
>>> problem is?
>>> ==>
>>> my problem is recon-all -i
>>> didn't working...
>>> so, if i type the recon-all
>>> -i~then show up theses
>>>
>>> 
>>> ERROR: 32512, see
>>>
>>> /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out
>>> for
>>> more details
>>> Linux localhost.localdomain
>>> 2.6.32-504.el6.x86_64 #1
>>> SMP Wed Oct 15 04:27:16
>>> UTC 2014 x86_64 x86_64
>>> x86_64 GNU/Linux
>>> 
>>> dcmdjpeg.fs: error while
>>> loading shared libraries:
>>> libijg8.so.3.6: cannot
>>> open shared object file: No
>>> such file or directory
>>>
>>> +
>>> 
>>> then, i click the
>>>
>>>  root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out,
>>> show
>>> up
>>> these
>>>

Re: [Freesurfer] hello freesurfer developer~

[A-reum Min]

Hi, Bruce

When i use a Qdec, this message(12.png) show up..
How can i solve this problem?

2015-07-23 22:57 GMT+09:00 Bruce Fischl :

> 1. No, each subject has a different #. You can map to fsaverage (this is
> what -qcache does if you specify it for recon-all), then they will have the
> same #.
>
> 2. What result data do you mean?
>
> 3. Yes, although I'll leave the details to Doug (since I don't remember
> how his cluster code works).
>
> 4. The significance doesn't depend on the cluster size unless you do
> multiple comparison corrections (and even then only if you do them a
> certain way)
>
> cheers
> Bruce
>
>
> On Thu, 23 Jul 2015, A-reum Min wrote:
>
>  HELLO developer
>> I have some question to you..
>>
>> 1. Every patient is given to the same number of vertex?
>>
>> 2. When i use a Qdec, How can I get the subject result data?
>>
>> 3. Could i get the significant vertex’s number, extent of the
>> significant area and gray matter volume?
>>
>> 4. Is it significant blue color which how many connected vertex?
>>
>>
>> 2015-05-29 2:03 GMT+09:00 A-reum Min :
>>   hello developer~
>> reconstruction is well done, so i'm doing on 'qdec' step..
>> Actually, i don't know how to treat the Design menu exactly..
>>
>> ---
>> Discrete(fixed factors) : diagnosis
>> continuous (covariate) : age , Left-Lateral-Ventricle
>>
>> ---
>> which one click before analyze?
>>
>> age range is 12years~24years/
>> all subjects are adolescent.
>> and no outlier in age range.. so.. age (continuous factor) does not
>> nasessart?
>>
>>
>> 2015-05-29 1:19 GMT+09:00 A-reum Min :
>>   hello developer~
>> reconstruction is well done, so i'm doing on 'qdec' step..
>> Actually, i don't know how to treat the Design menu exactly..
>>
>> ---
>> Discrete(fixed factors) : diagnosis
>> continuous (covariate) : age , Left-Lateral-Ventricle
>>
>> ---
>> which one click before analyze?
>>
>>
>>
>> 2015-04-05 21:41 GMT+09:00 Bruce Fischl
>> :
>>   I'm glad it worked out
>>   Bruce
>>   On Sun, 5 Apr 2015, A-reum Min wrote:
>>
>> Hello Bruce~
>> You're right.. my PISA dicom file header
>> is too short
>> so, freesurfer didn't read it.
>>
>> Therefore I use another subjects dicom
>> file and then freesurfer read it!
>>
>> thank you for u r adavice to me.
>>
>> I really appreciate u
>>
>> 2015-04-05 7:08 GMT+09:00 Bruce Fischl
>> :
>>   Hi  A-reum
>>
>>   the problem is that newer versions
>> of scanner software compress
>>   dicoms and the version of FS you
>> have doesn't know how to read
>>   it. So you need to decompress them
>> before passing them to
>>   recon-all
>>
>>   cheers
>>   Bruce
>>   On Sun, 5 Apr 2015, A-reum Min
>> wrote:
>>
>> Hello developer~
>>
>> Can you summarize what the
>> problem is?
>> ==>
>> my problem is recon-all -i
>> didn't working...
>> so, if i type the recon-all
>> -i~then show up theses
>>
>> 
>> ERROR: 32512, see
>>
>> /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out
>> for
>> more details
>> Linux localhost.localdomain
>> 2.6.32-504.el6.x86_64 #1
>> SMP Wed Oct 15 04:27:16
>> UTC 2014 x86_64 x86_64
>> x86_64 GNU/Linux
>>
>> dcmdjpeg.fs: error while
>> loading shared libraries:
>> libijg8.so.3.6: cannot
>> open shared object file: No
>> such file or directory
>>
>> +
>>
>> then, i click the
>>
>>  root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out,
>> show
>> up
>> these
>> dcmdjpeg.fs: error while
>> loading shared libraries:
>> libijg8.so.3.6: cannot
>> open shared object file: No
>> such file or directory
>>
>> Are you trying to read
>> compressed dicom?
>> ==>
>> Am 

Re: [Freesurfer] bad registration using mri_vol2vol

[Barbour, Tracy,M.D.]

I made the label in tkmedit, then i used label2v

Sent from my iPhone

> On Jul 24, 2015, at 12:22 PM, Douglas Greve  wrote:
> 
> Sorry, I've lost track of what is going on here. How was
> 
> lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.mgz
> 
> created?
> 
> 
>> On 7/23/15 12:08 PM, Barbour, Tracy,M.D. wrote:
>> Thank you Doug
>> 
>> I tried the way you suggested and the registration actually looks worse. I 
>> also tried:
>> 
>> mri_label2vol --subject fsaverage --label 
>> /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53/fsaverage_copy/label/$label.label
>>  --o $TARGET_DIR/tracy2_$label.nii.gz --reg 
>> $FREESURFER_HOME/average/mni152.register.dat --temp 
>> /autofs/cluster/maury/users/gcoombs/College_Risk/fcMRI/N12Trio_avg152T1.nii.gz
>> 
>> Is there a step that I am missing? This is for an amygdala functional ROI 
>> that was created in tkmedit and saved as a label.
>> 
>> Tracy
>> 
>> 
>> 
>> 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: Monday, July 20, 2015 2:28 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] bad registration using mri_vol2vol
>> 
>> where did lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.mgz come from?
>> It must be in the space of $SUBJECTS_DIR/fsaverage/mri/orig.mgz for that
>> transform to work
>> 
>>> On 07/17/2015 02:43 PM, Barbour, Tracy,M.D. wrote:
>>> 
>>> Hello,
>>> 
>>> I'm trying to convert an ROI mask I created in MNI305 space to MNI152.
>>> After running MRI_vol2vol the registration looks off (too anterior).
>>> 
>>> Here are my commands:
>>> 
>>> mri_convert -ot nii lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.mgz
>>> lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.nii
>>> 
>>> mri_vol2vol --mov
>>> /autofs/cluster/maury/users/gcoombs/College_Risk/fcMRI/N12Trio_avg152T1.nii.gz
>>> --targ lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.nii --inv
>>> --interp nearest --reg $FREESURFER_HOME/average/mni152.register.dat
>>> --o new_lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.nii.gz
>>> 
>>> Any ideas why the registration is off?
>>> 
>>> Tracy
>>> 
>>> 
>>> 
>>> ___
>>> 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
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] QDEC question

[Dr Sampada Sinha]

Hello Dr Greve,

Many thanks for replying to me. We are not including eTIV as a covariate.
Since we did not find any correlation with the thickness.

Kind regards,

Sampada
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[Freesurfer] Regarding: 3 groups and 1 covariate contrast

[Dr Sampada Sinha]

Dear freesurfer experts,

I am trying to  find group difference (thickness) among 3 groups (SCA1,
SCA2, SCA3) taking in account one covariate (CAG levels).  Will you please
let me know if I need to use DODS or DOSS, though I am more interested in
using DODS. I read the FSGD examples page (
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V) and I made the fsgd
file (One Factor/Three Levels), one Covariate (please see the attached fsgd
file). Now, my problem is how to create the contrast file. I know with DODS
Nregressors will be 6. How do I create the contrasts matrix to run the
mri_glmfit command?

I could create only three .mtx file, which are:
3 classes 1 variable

contrast 1.mtx - diff SCA1 vs SCA2 1 -1 0 0 0 0
contrast 2.mtx - diff SCA1 vs SCA3 1 0 -1 0 0 0
contrast 3.mtx - diff SCA2 vs SCA3 0 1 -1 0 0 0

Will you please let me know what other three contrasts matrix I should
add?I did go through the freesurfer forum and found this one query
particularly related to the same problem I am having
(http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33172.html).
Do I go by this contrasts matrix format which Stefania has come up with?

Forever appreciative of all your efforts and time given to me.





-- 
​S
​ampada
AIIMS, New Delhi​


g3v1.fsgd
Description: Binary data
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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
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