Re: [Freesurfer] Problem in Installing FreeSurfer on Mint19

[Maedeh Khalilian]

External Email - Use Caution

Dear Tim,
I did it successfully,
Thanks more...
Best
Maedeh___
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[Freesurfer] create ctab from annot

[Winkelbeiner, Stephanie A]

External Email - Use Caution

Hi freesurfer-experts,

I used a customized script that produces a more fine-grained parcellation 
resulting in an .annot file.
I don't seem to have a look-up-table (LUT), however.

I tried the following:

-  mri_annotation2label --> allows me to extract the single labels. But 
I rather need a .ctab file when I want to read out my values.

-  mris_anatomical_stats with the -c flag --> to output the colortable 
as a text file I first need the .ctab file.

Is there a way to get the LUT in a text file or the .ctab file just from the 
annotation file?

Thanks a lot in advance!
Cheers,
Stephanie

Stephanie Winkelbeiner, MSc
Research Coordinator
Psychiatry Research
Zucker Hillside Hospital
75-59 263 Street
Glen Oaks, NY 11004
Tel: (718) 470-4588
Email: swinkel...@northwell.edu

Northwell Health
Visit us at Northwell.edu



The information contained in this electronic e-mail transmission and any 
attachments are intended only for the use of the individual or entity to whom 
or to which it is addressed, and may contain information that is privileged, 
confidential and exempt from disclosure under applicable law. If the reader of 
this communication is not the intended recipient, or the employee or agent 
responsible for delivering this communication to the intended recipient, you 
are hereby notified that any dissemination, distribution, copying or disclosure 
of this communication and any attachment is strictly prohibited. If you have 
received this transmission in error, please notify the sender immediately by 
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Re: [Freesurfer] create ctab from annot

[Bruce Fischl]

Hi Stephanie

can you give us some details about how you generated your fine-grained 
parcellation?


cheers
Bruce
On Mon, 3 Dec 2018, Winkelbeiner, Stephanie A wrote:



External Email - Use Caution

Hi freesurfer-experts,

 

I used a customized script that produces a more fine-grained parcellation 
resulting in an .annot
file.

I don’t seem to have a look-up-table (LUT), however.

 

I tried the following:

-  mri_annotation2label à allows me to extract the single labels. But I 
rather need a .ctab
file when I want to read out my values.

-  mris_anatomical_stats with the –c flag à to output the colortable as 
a text file I first
need the .ctab file.

 

Is there a way to get the LUT in a text file or the .ctab file just from the 
annotation file?

 

Thanks a lot in advance!

Cheers,

Stephanie

 

Stephanie Winkelbeiner, MSc

Research Coordinator

Psychiatry Research

Zucker Hillside Hospital

75-59 263 Street

Glen Oaks, NY 11004

Tel: (718) 470-4588

Email: swinkel...@northwell.edu

 

Northwell Health

Visit us at Northwell.edu

 


The information contained in this electronic e-mail transmission and any 
attachments are intended
only for the use of the individual or entity to whom or to which it is 
addressed, and may contain
information that is privileged, confidential and exempt from disclosure under 
applicable law. If the
reader of this communication is not the intended recipient, or the employee or 
agent responsible for
delivering this communication to the intended recipient, you are hereby 
notified that any
dissemination, distribution, copying or disclosure of this communication and 
any attachment is
strictly prohibited. If you have received this transmission in error, please 
notify the sender
immediately by telephone and electronic mail, and delete the original 
communication and any
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Receipt by anyone other than the intended recipient is not a waiver of any 
attorney-client,
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Re: [Freesurfer] create ctab from annot

[Greve, Douglas N.,Ph.D.]

You can use mri_annotation2label to extract a color table from the 
annotation

On 12/03/2018 07:06 PM, Bruce Fischl wrote:
> Hi Stephanie
>
> can you give us some details about how you generated your fine-grained 
> parcellation?
>
> cheers
> Bruce
> On Mon, 3 Dec 2018, Winkelbeiner, Stephanie A wrote:
>
>>
>> External Email - Use Caution
>>
>> Hi freesurfer-experts,
>>
>>
>>
>> I used a customized script that produces a more fine-grained 
>> parcellation resulting in an .annot
>> file.
>>
>> I don’t seem to have a look-up-table (LUT), however.
>>
>>
>>
>> I tried the following:
>>
>> -  mri_annotation2label à allows me to extract the single 
>> labels. But I rather need a .ctab
>> file when I want to read out my values.
>>
>> -  mris_anatomical_stats with the –c flag à to output the 
>> colortable as a text file I first
>> need the .ctab file.
>>
>>
>>
>> Is there a way to get the LUT in a text file or the .ctab file just 
>> from the annotation file?
>>
>>
>>
>> Thanks a lot in advance!
>>
>> Cheers,
>>
>> Stephanie
>>
>>
>>
>> Stephanie Winkelbeiner, MSc
>>
>> Research Coordinator
>>
>> Psychiatry Research
>>
>> Zucker Hillside Hospital
>>
>> 75-59 263 Street
>>
>> Glen Oaks, NY 11004
>>
>> Tel: (718) 470-4588
>>
>> Email: swinkel...@northwell.edu
>>
>>
>>
>> Northwell Health
>>
>> Visit us at Northwell.edu
>>
>>
>>
>>
>> The information contained in this electronic e-mail transmission and 
>> any attachments are intended
>> only for the use of the individual or entity to whom or to which it 
>> is addressed, and may contain
>> information that is privileged, confidential and exempt from 
>> disclosure under applicable law. If the
>> reader of this communication is not the intended recipient, or the 
>> employee or agent responsible for
>> delivering this communication to the intended recipient, you are 
>> hereby notified that any
>> dissemination, distribution, copying or disclosure of this 
>> communication and any attachment is
>> strictly prohibited. If you have received this transmission in error, 
>> please notify the sender
>> immediately by telephone and electronic mail, and delete the original 
>> communication and any
>> attachment from any computer, server or other electronic recording or 
>> storage device or medium.
>> Receipt by anyone other than the intended recipient is not a waiver 
>> of any attorney-client,
>> physician-patient or other privilege.
>>
>
>
> ___
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[Freesurfer] volume and mean intensity values from single nii file with multiple ROIs

[Anik Dar]

External Email - Use Caution

Dear All,

I have segmented the midbrain of each subjects into different subregions
(peduncle, substantia nigra, red nucleus etc) using an atlas. I am trying
to extract the volume of each region (the regions are labeled 101, 102, 103
etc) and also trying to extract the mean intensity from MPRAGE from each of
these regions.

Is there a way to do this in freesurfer tools ? I realize that there is no
color lut / index file associated with this atlas in freesurfer.

Please let me know.

Thank you,

Ani
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[Freesurfer] Surface displacement

[1013364183]

External Email - Use Caution

Dear FS,
 We want to calculate the displacement of different surfaces, what should we do?


yours yujunjie___
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Re: [Freesurfer] When no control points are needed...

[Bruce Fischl]

Hi Rosalia

you always have to run autorecon3 every time autorecon2 is run

cheers
Bruce


On Mon, 3 Dec 2018, Rosalia 
Dacosta Aguayo wrote:




External Email - Use Caution

Dear Bruce and Bram,

After improving the pial surface for my participants, I have seen that some of 
them do not need
control points. My question is: for those ones, should I run -autorecon2 and 
-autorecon3 or only
-autorecon3.

Hi Bruce and Bram, I will try to upload two problematic files. When I told you 
that I have been
editing all my participants I was referring that some of them need more editing 
than others, and the
ones that needed the less I just tried to improve the pial surface not too 
much, but now the results
are better than before.

Thank you in advance for your help.Yours sincerely,
Rosalia

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[Freesurfer] mris_preproc paired diff outputs 0 values

[Sims, Sara A]

External Email - Use Caution

Hello,
I am trying to do a paired difference analysis of two runs of probtrackx (I 
have already put them on the surface). The two conditions are “central” and 
“far” for each subject. I have already checked the individual subjects data and 
it does indeed have values.

Here is a sample of my subject list:
100206.central
100206.far
100307.central
100307.far
100408.central
100408.far
…etc.

Here is my mris_preproc script:
mris_preproc --target fsaverage --hemi lh --isp 
$in/FP/100206.central/lhsurf.mgh --isp $in/FP/100206.far/lhsurf.mgh --isp 
$in/FP/100307.central/lhsurf.mgh --isp $in/FP/100307.far/lhsurf.mgh --isp 
$in/FP/100408.central/lhsurf.mgh --isp $in/FP/100408.far/lhsurf.mgh … --out 
$out/preproc_FP_cf_lh/lh.paired-diff.FP_cf.mgh --f $sublist --paired-diff

The output log shows no errors, the number of inputs equals the number in the 
subject list and it creates a file but it’s all zeros. I just have no idea as 
to why this would happen?

Thanks,

Sara Sims

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Re: [Freesurfer] When no control points are needed...

[Rosalia Dacosta Aguayo]

External Email - Use Caution

Hi Bruce,

Sorry for double posting.
I am advancing, but there is still some point I am missing. I would greatly
appreciate your help:

rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ cd
/home/rosalia/Desktop/transferrosalia@rosalia-Lenovo-Y520-15IKBN
~/Desktop/transfer $ ftp surfer.nmr.mgh.harvard.edu
Connected to surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this
site
220-shows implicit consent to our Acceptable Use Policy outlined
at
220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php

220-
220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220-   and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220-  try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:rosalia): anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> two_different_problems.txt
?Invalid command
ftp>


On Mon, Dec 3, 2018 at 4:06 PM Rosalia Dacosta Aguayo 
wrote:

> Hi Bruce,
>
> Thank you for your reply.
> I am having problems when trying to upload the two files with FTP, it
> seems the problem is with the directory.
> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ ftp
> surfer.nmr.mgh.harvard.edu
> Connected to surfer.nmr.mgh.harvard.edu.
> 220-This is the Martinos Center Anonymous FTP service. Use of this
> site
> 220-shows implicit consent to our Acceptable Use Policy outlined
> at
> 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
>
> 220-
> 220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
> 220-
> 220-229 Entering Extended Passive Mode
> 220-
> 220-   and nothing happens OR
> 220-
> 220-229 Entering Extended Passive Mode
> 220-500 Bad EPRT protocol.
> 220-
> 220-  try issuing the EPSV command prior to GET or PUT.
> 220-
> 220
> Name (surfer.nmr.mgh.harvard.edu:rosalia): anonymous
> 331 Please specify the password.
> Password:
> 230 Login successful.
> Remote system type is UNIX.
> Using binary mode to transfer files.
> ftp> cd home/rosalia/Desktop/transfer
> 550 Failed to change directory.
> ftp>
>
>
> On Mon, Dec 3, 2018 at 3:50 PM Bruce Fischl 
> wrote:
>
>> Hi Rosalia
>>
>> you always have to run autorecon3 every time autorecon2 is run
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 3 Dec 2018, Rosalia
>> Dacosta Aguayo wrote:
>>
>> >
>> > External Email - Use Caution
>> >
>> > Dear Bruce and Bram,
>> >
>> > After improving the pial surface for my participants, I have seen that
>> some of them do not need
>> > control points. My question is: for those ones, should I run
>> -autorecon2 and -autorecon3 or only
>> > -autorecon3.
>> >
>> > Hi Bruce and Bram, I will try to upload two problematic files. When I
>> told you that I have been
>> > editing all my participants I was referring that some of them need more
>> editing than others, and the
>> > ones that needed the less I just tried to improve the pial surface not
>> too much, but now the results
>> > are better than before.
>> >
>> > Thank you in advance for your help.Yours sincerely,
>> > Rosalia
>> >
>> >___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] FTP issues [was: When no control points are needed...]

[ts+ml]

External Email - Use Caution

That looks fine. You are logged in and you changed the directory. Just put the 
file now:
 
   put 

(In general the command depends on your FTP client, but a 'put' command should 
be available in every FTP client I guess.) 

A general note: you may be better off using a graphical FTP client. Depending 
on your Operating System, you may want to try something like WinSCP, FileZilla 
Client, or CyberDuck.

> On December 3, 2018 at 4:33 PM Rosalia Dacosta Aguayo  
> wrote:
> 
> 
> External Email - Use Caution
> 
> Hi Bruce,
> 
> Sorry for double posting.
> I am advancing, but there is still some point I am missing. I would greatly
> appreciate your help:
> 
> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ cd
> /home/rosalia/Desktop/transferrosalia@rosalia-Lenovo-Y520-15IKBN
> ~/Desktop/transfer $ ftp surfer.nmr.mgh.harvard.edu
> Connected to surfer.nmr.mgh.harvard.edu.
> 220-This is the Martinos Center Anonymous FTP service. Use of this
> site
> 220-shows implicit consent to our Acceptable Use Policy outlined
> at
> 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
> 
> 220-
> 220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
> 220-
> 220-229 Entering Extended Passive Mode
> 220-
> 220-   and nothing happens OR
> 220-
> 220-229 Entering Extended Passive Mode
> 220-500 Bad EPRT protocol.
> 220-
> 220-  try issuing the EPSV command prior to GET or PUT.
> 220-
> 220
> Name (surfer.nmr.mgh.harvard.edu:rosalia): anonymous
> 331 Please specify the password.
> Password:
> 230 Login successful.
> Remote system type is UNIX.
> Using binary mode to transfer files.
> ftp> cd transfer/incoming
> 250 Directory successfully changed.
> ftp> two_different_problems.txt
> ?Invalid command
> ftp>
> 
> 
> On Mon, Dec 3, 2018 at 4:06 PM Rosalia Dacosta Aguayo 
> wrote:
> 
> > Hi Bruce,
> >
> > Thank you for your reply.
> > I am having problems when trying to upload the two files with FTP, it
> > seems the problem is with the directory.
> > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ ftp
> > surfer.nmr.mgh.harvard.edu
> > Connected to surfer.nmr.mgh.harvard.edu.
> > 220-This is the Martinos Center Anonymous FTP service. Use of this
> > site
> > 220-shows implicit consent to our Acceptable Use Policy outlined
> > at
> > 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
> >
> > 220-
> > 220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
> > 220-
> > 220-229 Entering Extended Passive Mode
> > 220-
> > 220-   and nothing happens OR
> > 220-
> > 220-229 Entering Extended Passive Mode
> > 220-500 Bad EPRT protocol.
> > 220-
> > 220-  try issuing the EPSV command prior to GET or PUT.
> > 220-
> > 220
> > Name (surfer.nmr.mgh.harvard.edu:rosalia): anonymous
> > 331 Please specify the password.
> > Password:
> > 230 Login successful.
> > Remote system type is UNIX.
> > Using binary mode to transfer files.
> > ftp> cd home/rosalia/Desktop/transfer
> > 550 Failed to change directory.
> > ftp>
> >
> >
> > On Mon, Dec 3, 2018 at 3:50 PM Bruce Fischl 
> > wrote:
> >
> >> Hi Rosalia
> >>
> >> you always have to run autorecon3 every time autorecon2 is run
> >>
> >> cheers
> >> Bruce
> >>
> >>
> >> On Mon, 3 Dec 2018, Rosalia
> >> Dacosta Aguayo wrote:
> >>
> >> >
> >> > External Email - Use Caution
> >> >
> >> > Dear Bruce and Bram,
> >> >
> >> > After improving the pial surface for my participants, I have seen that
> >> some of them do not need
> >> > control points. My question is: for those ones, should I run
> >> -autorecon2 and -autorecon3 or only
> >> > -autorecon3.
> >> >
> >> > Hi Bruce and Bram, I will try to upload two problematic files. When I
> >> told you that I have been
> >> > editing all my participants I was referring that some of them need more
> >> editing than others, and the
> >> > ones that needed the less I just tried to improve the pial surface not
> >> too much, but now the results
> >> > are better than before.
> >> >
> >> > Thank you in advance for your help.Yours sincerely,
> >> > Rosalia
> >> >
> >> >___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> ___
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-- 
Tim

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Re: [Freesurfer] When no control points are needed...

[Rosalia Dacosta Aguayo]

External Email - Use Caution

Hi Bruce,

This is the directory where I have the data:

/home/rosalia/Desktop/transfer

And I changed the directory before doing FTP...and then asked again for the
directory and I wrote the same directory  and then when asked me for the
name of the file, I provided the name of the file.txt

Thank you,
Rosalia

On Mon, Dec 3, 2018 at 4:51 PM Bruce Fischl 
wrote:

> is that the right directory/path on your end?
>
> On Mon, 3 Dec 2018, Rosalia Dacosta
> Aguayo wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi Bruce,
> >
> > Thank you for your reply.
> > I am having problems when trying to upload the two files with FTP, it
> seems
> > the problem is with the directory.
> > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ ftp
> > surfer.nmr.mgh.harvard.edu
> > Connected to surfer.nmr.mgh.harvard.edu.
> > 220-This is the Martinos Center Anonymous FTP service. Use of this
> > site
> > 220-shows implicit consent to our Acceptable Use Policy outlined
> > at
> > 220-
> http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
> ?? ?
> > 220-
> > 220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
> > 220-
> > 220-229 Entering Extended Passive Mode
> > 220-
> > 220-   and nothing happens OR
> > 220-
> > 220-229 Entering Extended Passive Mode
> > 220-500 Bad EPRT protocol.
> > 220-
> > 220-  try issuing the EPSV command prior to GET or PUT.
> > 220-
> > 220
> > Name (surfer.nmr.mgh.harvard.edu:rosalia): anonymous
> > 331 Please specify the password.
> > Password:
> > 230 Login successful.
> > Remote system type is UNIX.
> > Using binary mode to transfer files.
> > ftp> cd home/rosalia/Desktop/transfer
> > 550 Failed to change directory.
> > ftp>
> >
> >
> > On Mon, Dec 3, 2018 at 3:50 PM Bruce Fischl 
> > wrote:
> >   Hi Rosalia
> >
> >   you always have to run autorecon3 every time autorecon2 is run
> >
> >   cheers
> >   Bruce
> >
> >
> >   On Mon, 3 Dec 2018, Rosalia
> >   Dacosta Aguayo wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Dear Bruce and Bram,
> >   >
> >   > After improving the pial surface for my participants, I have
> >   seen that some of them do not need
> >   > control points. My question is: for those ones, should I run
> >   -autorecon2 and -autorecon3 or only
> >   > -autorecon3.
> >   >
> >   > Hi Bruce and Bram, I will try to upload two problematic files.
> >   When I told you that I have been
> >   > editing all my participants I was referring that some of them
> >   need more editing than others, and the
> >   > ones that needed the less I just tried to improve the pial
> >   surface not too much, but now the results
> >   > are better than before.
> >   >
> >   > Thank you in advance for your help.Yours sincerely,
> >   > Rosalia
> >   >
> >   >___
> >   Freesurfer mailing list
> >   Freesurfer@nmr.mgh.harvard.edu
> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >___
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Re: [Freesurfer] Surface displacement

[Bruce Fischl]

Hi yujunjie

you need to give us more information than this.

cheers
Bruce
On Mon, 3 Dec 2018, 
1013364183 wrote:




External Email - Use Caution

Dear FS,
 We want to calculate the displacement of different surfaces, what should we
do?

yours yujunjie

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Re: [Freesurfer] When no control points are needed...

[Bruce Fischl]

is that the right directory/path on your end?

On Mon, 3 Dec 2018, Rosalia Dacosta 
Aguayo wrote:




External Email - Use Caution

Hi Bruce,

Thank you for your reply.
I am having problems when trying to upload the two files with FTP, it seems
the problem is with the directory.
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ ftp
surfer.nmr.mgh.harvard.edu
Connected to surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this
site
220-shows implicit consent to our Acceptable Use Policy outlined
at  
220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php 

?? ?

220-
220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220-   and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220-  try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:rosalia): anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd home/rosalia/Desktop/transfer
550 Failed to change directory.
ftp>


On Mon, Dec 3, 2018 at 3:50 PM Bruce Fischl 
wrote:
  Hi Rosalia

  you always have to run autorecon3 every time autorecon2 is run

  cheers
  Bruce


  On Mon, 3 Dec 2018, Rosalia
  Dacosta Aguayo wrote:

  >
  > External Email - Use Caution
  >
  > Dear Bruce and Bram,
  >
  > After improving the pial surface for my participants, I have
  seen that some of them do not need
  > control points. My question is: for those ones, should I run
  -autorecon2 and -autorecon3 or only
  > -autorecon3.
  >
  > Hi Bruce and Bram, I will try to upload two problematic files.
  When I told you that I have been
  > editing all my participants I was referring that some of them
  need more editing than others, and the
  > ones that needed the less I just tried to improve the pial
  surface not too much, but now the results
  > are better than before.
  >
  > Thank you in advance for your help.Yours sincerely,
  > Rosalia
  >
  >___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz

[Diamond, Bram Ryder]

I'm not sure why there is no error with the mri_convert function, but it 
somehow took in your BE2_T1.nii and creating a corrupted 001.mgz. The 
rawavg.mgz is just a copy of the 001.mgz, so it's no surprise that it has the 
same issues. You only get an error when recon-all attempts to run mri_convert 
on the rawavg.mgz.


The corrupted 001.mgz is only 8K - it should be more like 12M. I can't open it 
in Matlab with MRIread to see what might have gone wrong. I'm not sure what the 
problem is, but it is definitely local to whatever machine you are using to run 
recon-all. I've run the nifty you uploaded through recon-all using freesurfer 
5.3 without an issue on my machine.


Please let me know if downloading freesurfer again fixes the issue.


Best,

Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Batuhan Erkat 

Sent: Saturday, December 1, 2018 9:52:34 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: batuhan.er...@umram.bilkent.edu.tr; astev...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz


External Email - Use Caution

I will ask our admin to do so. I also don't have any problems on my personal 
computer, so my T1 image should be fine, but the problem starts at mri_convert 
function, which surprisingly gives no error. Is it possible for you to look at 
the 001.mgz and rawavg.mgz files and see what could be the problem with the 
mri_convert function?

Best,
Batuhan

On Sat, Dec 1, 2018 at 12:54 AM Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:

It's strange, but I'm not having the same issue. Can you try downloading 5.3 
again and see if that fixes your issue?


Bram


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Batuhan Erkat 
mailto:o.batuhaner...@gmail.com>>
Sent: Friday, November 30, 2018 12:49:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: 
batuhan.er...@umram.bilkent.edu.tr; 
astev...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz


External Email - Use Caution

Done

On Fri, Nov 30, 2018 at 8:46 PM Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:

Can you please upload the BE2_T1.nii?


Bram


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Batuhan Erkat 
mailto:o.batuhaner...@gmail.com>>
Sent: Thursday, November 29, 2018 12:35:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: 
batuhan.er...@umram.bilkent.edu.tr; 
astev...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz


External Email - Use Caution

Hi Bram,

I finally did it, thank you for your help, and sorry about my noobity!

ftp> put BE2.tar.xz
local: BE2.tar.xz remote: BE2.tar.xz
200 PORT command successful. Consider using PASV.
150 Ok to send data.
226 Transfer complete.
61572 bytes sent in 0.15 secs (402.3777 kB/s)

Best regards,
Batuhan

On Thu, Nov 29, 2018 at 5:36 PM Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:

I can't see any of your data. The problem is likely that you are feeding the 
full file path. Try using just the file name without the path. First cd to your 
data directory, then log on to the freesurfer FTP file exchange and follow the 
instructions on our wiki.

Thanks for your patience! I'll be updating our wiki documentation to be more 
clear.

Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Batuhan Erkat 
mailto:o.batuhaner...@gmail.com>>
Sent: Tuesday, November 27, 2018 10:28:23 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: 
batuhan.er...@umram.bilkent.edu.tr; 
astev...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz


External Email - Use Caution

I tried to put the subject folder in tar.xz format for ease, this is what I get:

ftp> put 

Re: [Freesurfer] Surface displacement

[1013364183]

External Email - Use Caution

Dear Bruce,


We resample the surface of the high resolution image to the low resolution 
image surface, then compare the surface of the original image to the resampled 
surface to calculate his surface displacement. What should we do?


-- Original --
From:  "Bruce Fischl";
Date:  Mon, Dec 3, 2018 11:49 PM
To:  "Freesurfer support list";

Subject:  Re: [Freesurfer] Surface displacement



Hi yujunjie

you need to give us more information than this.

cheers
Bruce
On Mon, 3 Dec 2018, 
1013364183 wrote:

> 
> External Email - Use Caution
> 
> Dear FS,
>  We want to calculate the displacement of different surfaces, what should we
> do?
> 
> yours yujunjie
> 
>
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[Freesurfer] Warping fsaverage maps to MNI152 volume

[Alon Baram]

External Email - Use Caution

Hello,

I have a significance map I obtained through some analysis I did in Matlab.
It's currently in fsaverage space. I want to move it to MNI152 space to
compare with other results. From exploring the archives, it seems there are
two ways of doing this, and I'm not sure which is better - any advice or
correction would be appreciated.

*Method 1*: First move to fsaverage volume, then us volumetc registraion to
move to MNI152:

1. mri_surf2vol --surfval sigMap.mgh --identity fsaverage --template
./fsaverage/mri/T1.mgz --hemi rh --o sigMap.fsspace.mgz


2. mri_vol2vol --inv --targ sigMap.fsspace.mgz --mov
/$FSL_DIR/data/standard/MNI152_T1_2mm.nii.gz --o sigMap_MNI.nii
--interp nearest --reg fsaverage/mri/transforms/reg.mni152.2mm.dat


*Method 2*: Run recon-all on the MNI152 T1 image. Use mri_surf2surf to map
to move sigMap to the MNI152 surface. Then use mri_surf2vol with the
--identity flag to move from MIN152 surface to volume.

I ran method 1 and it looks OK though in some place it seems the out put
doesn't follow white matter super nicely (though generally quite good). See
attached image.

I haven't ran method 2 yet.

Thanks very much!
Alon

[image: image.png]
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Re: [Freesurfer] When no control points are needed...

[Rosalia Dacosta Aguayo]

External Email - Use Caution

Hi Diamond!

I think I did it.
Thank you very much!!

 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/share/fsl/5.0
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ cd
/home/rosalia/Desktop/transferrosalia@rosalia-Lenovo-Y520-15IKBN
~/Desktop/transfer $ ftp surfer.nmr.mgh.harvard.edu
Connected to surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this
site
220-shows implicit consent to our Acceptable Use Policy outlined
at
220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php

220-
220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220-   and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220-  try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:rosalia): anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> put two_different_problems.tar.gz
local: two_different_problems.tar.gz remote: two_different_problems.tar.gz
200 PORT command successful. Consider using PASV.
150 Ok to send data.


On Mon, Dec 3, 2018 at 6:46 PM Diamond, Bram Ryder <
brdiam...@mgh.harvard.edu> wrote:

> Hi Rosalia,
>
>
> Within the FTP interface, you need to write
> "put two_different_problems.txt". It seems like you only wrote the file
> name. Also, the example we provide is "filename.txt", make sure you
> write your file name - only include ".txt" if your file has that extension.
>
>
> Let me know if you have any additional questions.
>
>
> Best,
>
> Bram
>
>
> *Bram R. Diamond, BSc*
> Research Technician II
> Laboratory for Computational Neuroimaging
> Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 149 13th Street
> Charlestown, MA 02129
> (p): 617-726-6598
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta
> Aguayo 
> *Sent:* Monday, December 3, 2018 10:54:53 AM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] When no control points are needed...
>
>
> External Email - Use Caution
>
> Hi Bruce,
>
> This is the directory where I have the data:
>
> /home/rosalia/Desktop/transfer
>
> And I changed the directory before doing FTP...and then asked again for
> the directory and I wrote the same directory  and then when asked me for
> the name of the file, I provided the name of the file.txt
>
> Thank you,
> Rosalia
>
> On Mon, Dec 3, 2018 at 4:51 PM Bruce Fischl 
> wrote:
>
> is that the right directory/path on your end?
>
> On Mon, 3 Dec 2018, Rosalia Dacosta
> Aguayo wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi Bruce,
> >
> > Thank you for your reply.
> > I am having problems when trying to upload the two files with FTP, it
> seems
> > the problem is with the directory.
> > rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ ftp
> > surfer.nmr.mgh.harvard.edu
> > Connected to surfer.nmr.mgh.harvard.edu.
> > 220-This is the Martinos Center Anonymous FTP service. Use of this
> > site
> > 220-shows implicit consent to our Acceptable Use Policy outlined
> > at
> > 220-
> http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
> ?? ?
> > 220-
> > 220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
> > 220-
> > 220-229 Entering Extended Passive Mode
> > 220-
> > 220-   and nothing happens OR
> > 220-
> > 220-229 Entering Extended Passive Mode
> > 220-500 Bad EPRT protocol.
> > 220-
> > 220-  try issuing the EPSV command prior to GET or PUT.
> > 220-
> > 220
> > Name (surfer.nmr.mgh.harvard.edu:rosalia): anonymous
> > 331 Please specify the password.
> > Password:
> > 230 Login successful.
> > Remote system type is UNIX.
> > Using binary mode to transfer files.
> > ftp> cd home/rosalia/Desktop/transfer
> > 550 Failed to change directory.
> > ftp>
> >
> >
> > On Mon, Dec 3, 2018 at 3:50 PM Bruce Fischl 
> > wrote:
> >   Hi Rosalia
> >
> >   you always have to run autorecon3 every time autorecon2 is run
> >
> >   cheers
> >   Bruce
> >
> >
> >   On Mon, 3 Dec 2018, Rosalia
> >   Dacosta Aguayo wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Dear Bruce and Bram,
> >   >
> >   > After improving the pial surface for my participants, I have
> >   seen that some of them do not need
> >  

Re: [Freesurfer] When no control points are needed...

[Diamond, Bram Ryder]

Hi Rosalia,


Within the FTP interface, you need to write "put two_different_problems.txt". 
It seems like you only wrote the file name. Also, the example we provide is 
"filename.txt", make sure you write your file name - only include ".txt" if 
your file has that extension.


Let me know if you have any additional questions.


Best,

Bram


Bram R. Diamond, BSc
Research Technician II
Laboratory for Computational Neuroimaging
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street
Charlestown, MA 02129
(p): 617-726-6598



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Rosalia Dacosta Aguayo 

Sent: Monday, December 3, 2018 10:54:53 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] When no control points are needed...


External Email - Use Caution

Hi Bruce,

This is the directory where I have the data:

/home/rosalia/Desktop/transfer

And I changed the directory before doing FTP...and then asked again for the 
directory and I wrote the same directory  and then when asked me for the name 
of the file, I provided the name of the file.txt

Thank you,
Rosalia

On Mon, Dec 3, 2018 at 4:51 PM Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
is that the right directory/path on your end?

On Mon, 3 Dec 2018, Rosalia Dacosta
Aguayo wrote:

>
> External Email - Use Caution
>
> Hi Bruce,
>
> Thank you for your reply.
> I am having problems when trying to upload the two files with FTP, it seems
> the problem is with the directory.
> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ ftp
> surfer.nmr.mgh.harvard.edu
> Connected to surfer.nmr.mgh.harvard.edu.
> 220-This is the Martinos Center Anonymous FTP service. Use of this
> site
> 220-shows implicit consent to our Acceptable Use Policy outlined
> at
> 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php
?? ?
> 220-
> 220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
> 220-
> 220-229 Entering Extended Passive Mode
> 220-
> 220-   and nothing happens OR
> 220-
> 220-229 Entering Extended Passive Mode
> 220-500 Bad EPRT protocol.
> 220-
> 220-  try issuing the EPSV command prior to GET or PUT.
> 220-
> 220
> Name (surfer.nmr.mgh.harvard.edu:rosalia): anonymous
> 331 Please specify the password.
> Password:
> 230 Login successful.
> Remote system type is UNIX.
> Using binary mode to transfer files.
> ftp> cd home/rosalia/Desktop/transfer
> 550 Failed to change directory.
> ftp>
>
>
> On Mon, Dec 3, 2018 at 3:50 PM Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>>
> wrote:
>   Hi Rosalia
>
>   you always have to run autorecon3 every time autorecon2 is run
>
>   cheers
>   Bruce
>
>
>   On Mon, 3 Dec 2018, Rosalia
>   Dacosta Aguayo wrote:
>
>   >
>   > External Email - Use Caution
>   >
>   > Dear Bruce and Bram,
>   >
>   > After improving the pial surface for my participants, I have
>   seen that some of them do not need
>   > control points. My question is: for those ones, should I run
>   -autorecon2 and -autorecon3 or only
>   > -autorecon3.
>   >
>   > Hi Bruce and Bram, I will try to upload two problematic files.
>   When I told you that I have been
>   > editing all my participants I was referring that some of them
>   need more editing than others, and the
>   > ones that needed the less I just tried to improve the pial
>   surface not too much, but now the results
>   > are better than before.
>   >
>   > Thank you in advance for your help.Yours sincerely,
>   > Rosalia
>   >
>   >___
>   Freesurfer mailing list
>   Freesurfer@nmr.mgh.harvard.edu
>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] When no control points are needed...

[Rosalia Dacosta Aguayo]

External Email - Use Caution

Hi Bruce,

Thank you for your reply.
I am having problems when trying to upload the two files with FTP, it seems
the problem is with the directory.
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ ftp
surfer.nmr.mgh.harvard.edu
Connected to surfer.nmr.mgh.harvard.edu.
220-This is the Martinos Center Anonymous FTP service. Use of this
site
220-shows implicit consent to our Acceptable Use Policy outlined
at
220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php

220-
220-OPERATIONAL NOTE:  If, when doing a GET or PUT, you encounter either
220-
220-229 Entering Extended Passive Mode
220-
220-   and nothing happens OR
220-
220-229 Entering Extended Passive Mode
220-500 Bad EPRT protocol.
220-
220-  try issuing the EPSV command prior to GET or PUT.
220-
220
Name (surfer.nmr.mgh.harvard.edu:rosalia): anonymous
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd home/rosalia/Desktop/transfer
550 Failed to change directory.
ftp>


On Mon, Dec 3, 2018 at 3:50 PM Bruce Fischl 
wrote:

> Hi Rosalia
>
> you always have to run autorecon3 every time autorecon2 is run
>
> cheers
> Bruce
>
>
> On Mon, 3 Dec 2018, Rosalia
> Dacosta Aguayo wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Bruce and Bram,
> >
> > After improving the pial surface for my participants, I have seen that
> some of them do not need
> > control points. My question is: for those ones, should I run -autorecon2
> and -autorecon3 or only
> > -autorecon3.
> >
> > Hi Bruce and Bram, I will try to upload two problematic files. When I
> told you that I have been
> > editing all my participants I was referring that some of them need more
> editing than others, and the
> > ones that needed the less I just tried to improve the pial surface not
> too much, but now the results
> > are better than before.
> >
> > Thank you in advance for your help.Yours sincerely,
> > Rosalia
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] Set annotation cluster color

[Ting Li]

External Email - Use Caution

Dear Freesurfer Expert,

Can I change the color of loading from the annot file in Freeview? Thanks a
lot!

Best regards,
Ting
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[Freesurfer] fMRI time series extraction

[Zhi Li]

External Email - Use Caution

Hello FreeSurfer Experts,

Now I have a custom annotation file (only the cortical surface). May I ask
how could I use it to extract the mean time series from the
fsfast-preprocessed fMRI data? I have tried to transform this annotation
file into anatomical volume first:

mri_aparc2aseg --s fsaverage --annot test --o test.mgz

It seems I cannot do it to the left and right surface respectively, right?
How should use this .mgz file next? Any suggestions would be appreciated.

Best wishes,

Zhi Li
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[Freesurfer] Problem in Installing FreeSurfer on Mint19

[Maedeh Khalilian]

External Email - Use Caution

Dear experts,
Thank u very much for all the help so far
I have   mint19 on my system and I have installed FreeSurfer on it.
when I run a command like "mri_convert" it is ok.
But when I run "recon-all" and some other commands, I see the error below :

bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No 
such file or directory
by the way my default setup file is .bashrc.
I really dunno what the problem is.I would be grateful if u could help me.
Cheers,
Maedeh___
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Re: [Freesurfer] Problem in Installing FreeSurfer on Mint19

[ts+ml]

External Email - Use Caution

Sounds like you do not have the tcsh shell installed on your system. There is 
no need to change your default shell from bash to tcsh, but you need tcsh 
installed for FreeSurfer to work.

Have your system admin install it. Since Mint is Debian-based, this should do 
it:

   sudo apt-get install tcsh

Best,

Tim

> On December 3, 2018 at 9:26 AM Maedeh Khalilian  
> wrote:
> 
> 
> External Email - Use Caution
> 
> Dear experts,
> Thank u very much for all the help so far
> I have   mint19 on my system and I have installed FreeSurfer on it.
> when I run a command like "mri_convert" it is ok.
> But when I run "recon-all" and some other commands, I see the error below :
> 
> bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No 
> such file or directory
> by the way my default setup file is .bashrc.
> I really dunno what the problem is.I would be grateful if u could help me.
> Cheers,
> Maedeh___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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[Freesurfer] When no control points are needed...

[Rosalia Dacosta Aguayo]

External Email - Use Caution

Dear Bruce and Bram,

After improving the pial surface for my participants, I have seen that some
of them do not need control points. My question is: for those ones, should
I run -autorecon2 and -autorecon3 or only -autorecon3.

Hi Bruce and Bram, I will try to upload two problematic files. When I told
you that I have been editing all my participants I was referring that some
of them need more editing than others, and the ones that needed the less I
just tried to improve the pial surface not too much, but now the results
are better than before.

Thank you in advance for your help.
Yours sincerely,
Rosalia
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