Dear MH
Thank you so much for your help.I have one more question if that's ok...I am
trying to work with compact data (gray ordinate time series data). However,as I
proceed to open them with mri cro(and mri cron) the following error prompts:
The header file is not in Analyze format [the first 4 bytes do not have the
value 348]. Assuming big-endian data.
Header describes an unknown data type.Bit pixels=256 Data Type=0Could you
please tell me what is wrong?Many thanks in advance.
Best,mahsa
On Tuesday, October 14, 2014 11:43 PM, "Harms, Michael" <[email protected]>
wrote:
Hi,For Workbench and 'wb_command', I'd suggest that you start with the
documentation and tutorials available at:http://humanconnectome.org/software/
If you are not familiar with CIFTI and the outputs we provide, it sounds like
you would also benefit by reviewing:http://humanconnectome.org/documentation/
For FSL, they have their own extensive set of documentation and tutorials that
you can take advantage of.
cheers,-MH
-- Michael Harms,
Ph.D.-----------------------------------------------------------Conte Center
for the Neuroscience of Mental DisordersWashington University School of
MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave. Tel:
314-747-6173St. Louis, MO 63110 Email: [email protected]
From: Mahsa Alizade shalchy <[email protected]>
Reply-To: Mahsa Alizade shalchy <[email protected]>
Date: Tuesday, October 14, 2014 3:07 PM
To: "Harms, Michael" <[email protected]>
Subject: Re: [HCP-Users] ROI extraction of rest fmri data
Sorry if my questions sound naive. I am a beginner in fmri(esp rfmri
)field.Since I'm working on Q1 data, I do not remember any "CIFTI/grayordinate
" versions of the data (There were 3 kinds of rfmri data namely as
preprocessed,fix,fix extended and I utilized the 3rd one to skip any
preprocessing step).I unfortunately have no idea about Workbench and
wb_command...Could I mask my data using FSL?Could you please explain a bit
more?Thank you in advance.
Best,mahsa
On Tuesday, October 14, 2014 11:27 PM, "Harms, Michael" <[email protected]>
wrote:
Hi,You are going to have a hard time working with the resting state volume data
in matlab.I'd suggest using the CIFTI/grayordinate versions of the data (which
are much more compact) and starting to familiarize yourself with the
capabilities of Workbench and 'wb_command'. In my experience, the various FSL
tools work, although again, if you are working with the volume data, just be
prepared that some operations are going to be slow.
cheers,-MH
-- Michael Harms,
Ph.D.-----------------------------------------------------------Conte Center
for the Neuroscience of Mental DisordersWashington University School of
MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave.Tel:
314-747-6173St. Louis, MO 63110Email:[email protected]
From: Mahsa Alizade shalchy <[email protected]>
Reply-To: Mahsa Alizade shalchy <[email protected]>
Date: Tuesday, October 14, 2014 2:49 PM
To: "Harms, Michael" <[email protected]>
Subject: Re: [HCP-Users] ROI extraction of rest fmri data
Dear MH
Thank you so much for replying.
My goal is to extract functional connectivity maps of my ROI.For task fmri
data I manually did " fmri data.*ROI " (using matlab). However, for rest fmri
data, due to large size this is not possible.I also tried 3dcalc of afni but
failed.Please let me know if you need further information.
Best,mahsa
On Tuesday, October 14, 2014 11:04 PM, "Harms, Michael" <[email protected]>
wrote:
Hi Mahsa,I think you are going to have to be more specific for anyone to be
able to help you. What is your goal? And what tools are you using and how
are you trying to apply the masking. For example, if you are trying to work
with the resting state volume data in Matlab/SPM, you may find that the file
sizes are too large to work conveniently in Matlab.
cheers,-MH
-- Michael Harms,
Ph.D.-----------------------------------------------------------Conte Center
for the Neuroscience of Mental DisordersWashington University School of
MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave.Tel:
314-747-6173St. Louis, MO 63110Email:[email protected]
From: Mahsa Alizade shalchy <[email protected]>
Reply-To: Mahsa Alizade shalchy <[email protected]>
Date: Tuesday, October 14, 2014 2:23 PM
To: Hcp-users <[email protected]>
Subject: [HCP-Users] ROI extraction of rest fmri data
Dear allHi
I'm working on the rest fmri data(fix extended) and I have a problem regarding
masking. Since the data is very large (4D image with 1200 volumes), I could not
apply masking.Could you please help me on this matter?Many thanks in
advance.Ps:I have 8 G of RAM available.
Best,mahsa
_______________________________________________
HCP-Users mailing list
[email protected]
http://lists.humanconnectome.org/mailma n/listinfo/hcp-users The materials in
this message are private and may contain Protected Healthcare Information or
other information of a sensitive nature. If you are not the intended recipient,
be advised that any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly prohibited.
If you have received this email in error, please immediately notify the sender
via telephone or return mail.
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
The materials in this message are private and may contain Protected
Healthcare Information or other information of a sensitive nature. If you are
not the intended recipient, be advised that any unauthorized use, disclosure,
copying or the taking of any action in reliance on the contents of this
information is strictly prohibited. If you have received this email in error,
please immediately notify the sender via telephone or return mail.
_______________________________________________
HCP-Users mailing list
[email protected]
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Spam detection software, running on the system "mailman02.nrg.mir", has
identified this incoming email as possible spam. The original message
has been attached to this so you can view it (if it isn't spam) or label
similar future email. If you have any questions, see
@@CONTACT_ADDRESS@@ for details.
Content preview: Dear MH Thank you so much for your help.I have one more
question
if that's ok...I am trying to work with compact data (gray ordinate time
series data). However,as I proceed to open them with mri cro(and mri cron)
the following error prompts: The header file is not in Analyze format [the
first 4 bytes do not have the value 348]. Assuming big-endian data. Header
describes an unknown data type.Bit pixels=256 Data Type=0Could you please
tell me what is wrong?Many thanks in advance. Best,mahsa [...]
Content analysis details: (5.1 points, 5.0 required)
pts rule name description
---- ---------------------- --------------------------------------------------
0.0 FREEMAIL_FROM Sender email is freemail (ma.shalchy[at]yahoo.com)
(mailer-daemon[at]googlemail.com)
(mailer-daemon[at]googlemail.com)
(ma.shalchy[at]yahoo.com)
2.4 FORGED_YAHOO_RCVD 'From' yahoo.com does not match 'Received' headers
2.7 FRT_ROLEX BODY: ReplaceTags: Rolex
0.0 HTML_MESSAGE BODY: HTML included in message
0.0 T_DKIM_INVALID DKIM-Signature header exists but is not valid
Spam detection software, running on the system "mailman02.nrg.mir", has
identified this incoming email as possible spam. The original message
has been attached to this so you can view it (if it isn't spam) or label
similar future email. If you have any questions, see
@@CONTACT_ADDRESS@@ for details.
Content preview: Dear MH Thank you so much for your help.I have one more
question
if that's ok...I am trying to work with compact data (gray ordinate time
series data). However,as I proceed to open them with mri cro(and mri cron)
the following error prompts: The header file is not in Analyze format [the
first 4 bytes do not have the value 348]. Assuming big-endian data. Header
describes an unknown data type.Bit pixels=256 Data Type=0Could you please
tell me what is wrong?Many thanks in advance. Best,mahsa [...]
Content analysis details: (5.1 points, 5.0 required)
pts rule name description
---- ---------------------- --------------------------------------------------
0.0 FREEMAIL_FROM Sender email is freemail (ma.shalchy[at]yahoo.com)
(mailer-daemon[at]googlemail.com)
(mailer-daemon[at]googlemail.com)
(ma.shalchy[at]yahoo.com)
(ma.shalchy[at]yahoo.com)
(ma.shalchy[at]yahoo.com)
(ma.shalchy[at]yahoo.com)
2.4 FORGED_YAHOO_RCVD 'From' yahoo.com does not match 'Received' headers
2.7 FRT_ROLEX BODY: ReplaceTags: Rolex
0.0 HTML_MESSAGE BODY: HTML included in message
0.0 MIME_QP_LONG_LINE RAW: Quoted-printable line longer than 76 chars
