from:"Jacobs H \(NP\)"

Aha, Ok, I will try to get my hands on that data and give it a go.
Thanks for the help!
Heidi

On 6/1/16, 4:01 AM, "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu>
wrote:

>
>The input needs to be the diffusion-weighted images, not the FA, MD, etc.
>There should be as many volumes in this input nifti as there are b-values
>in bval file and gradient vectors in the bvec file. The image
>registration, tractography, etc etc is performed on the
>diffusion-weighted
>images, not on the FA, MD, etc. The FA, MD, etc are used only in the very
>end, to extract FA, MD, etc for each tract. But to get the tracts in the
>first place, you need the images.
>
>On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Yes, each nifti contains one volume. I have different nifti’s for the
>> different metrics (FA, MD,..)
>> Is there a way I can use the trac-all on these files?
>>
>> On 5/31/16, 9:26 PM, "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu>
>> wrote:
>>
>>>
>>> Some of the errors make me suspect that your input DWI files contain
>>>only
>>> one volume. Could this be the case?
>>>
>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>
>>>> Hmm, weird, as I put a #  in front of it. Putting the eddy current to
>>>>0
>>>> gives the same error. Enclosed is the config file.
>>>> Thank you so much
>>>> Heidi
>>>>
>>>> On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>>> of
>>>> Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>>>of
>>>> ayend...@nmr.mgh.harvard.edu> wrote:
>>>>
>>>>>
>>>>> Hi Heidi - It knows where to find the freesurfer recons of the T1's
>>>>> from
>>>>> SUBJECTS_DIR (see example config file). Based on your log file, it
>>>>> looks
>>>>> like you haven't turned off the eddy current compensation, because
>>>>>it's
>>>>> trying to run it. If you attach your config file, I'll take a look.
>>>>>
>>>>> Best,
>>>>> a.y
>>>>>
>>>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>>>
>>>>>> Thanks! I tried to adapt the configuration file and it got a bit
>>>>>> further,
>>>>>> but then crashes again. Not sure why? I have added the log file, so
>>>>>> that
>>>>>> maybe you could have a look at what is happening?
>>>>>> Also, how does the trac-all command knows where to find the T1 data?
>>>>>> Thanks
>>>>>> Heidi
>>>>>>
>>>>>> On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on
>>>>>>behalf
>>>>>> of
>>>>>> Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>>>>> of
>>>>>> ayend...@nmr.mgh.harvard.edu> wrote:
>>>>>>
>>>>>>>
>>>>>>> No, it should be pointed to the DWI data, which can be corrected
>>>>>>> niftis
>>>>>>> instead of the original dicoms. I would recommend turning off all
>>>>>>>the
>>>>>>> corrections in the configuration file, and then running everything
>>>>>>> without
>>>>>>> skipping steps. This will create all the files that are expected to
>>>>>>> be
>>>>>>> there for the registration.
>>>>>>>
>>>>>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>>>>>
>>>>>>>> Dear Anastasia,
>>>>>>>>
>>>>>>>> Thanks for the feedback. So, does this mean that the dcm root
>>>>>>>>should
>>>>>>>> be
>>>>>>>> pointed towards the T1¹s? I have the FreeSurfer recon-all output
>>>>>>>>in
>>>>>>>> a
>>>>>>>> different folder.
>>>>>>>> Enclosed is the log file (of one subject) and the configuration
>>>>>>>> file.
>>>>>>>> You
>>>>>>>> will see that I tried the inter and intra option, because I
>>>>>>>>thought
>>>>>>>> that
>>>>>>>> for the inter it would not need anything else tha

Re: [Freesurfer] Tracula skip steps

Yes, each nifti contains one volume. I have different nifti’s for the
different metrics (FA, MD,..)
Is there a way I can use the trac-all on these files?

On 5/31/16, 9:26 PM, "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu>
wrote:

>
>Some of the errors make me suspect that your input DWI files contain only
>one volume. Could this be the case?
>
>On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Hmm, weird, as I put a #  in front of it. Putting the eddy current to 0
>> gives the same error. Enclosed is the config file.
>> Thank you so much
>> Heidi
>>
>> On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>of
>> Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
>> ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> Hi Heidi - It knows where to find the freesurfer recons of the T1's
>>>from
>>> SUBJECTS_DIR (see example config file). Based on your log file, it
>>>looks
>>> like you haven't turned off the eddy current compensation, because it's
>>> trying to run it. If you attach your config file, I'll take a look.
>>>
>>> Best,
>>> a.y
>>>
>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>
>>>> Thanks! I tried to adapt the configuration file and it got a bit
>>>> further,
>>>> but then crashes again. Not sure why? I have added the log file, so
>>>>that
>>>> maybe you could have a look at what is happening?
>>>> Also, how does the trac-all command knows where to find the T1 data?
>>>> Thanks
>>>> Heidi
>>>>
>>>> On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>>> of
>>>> Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>>>of
>>>> ayend...@nmr.mgh.harvard.edu> wrote:
>>>>
>>>>>
>>>>> No, it should be pointed to the DWI data, which can be corrected
>>>>>niftis
>>>>> instead of the original dicoms. I would recommend turning off all the
>>>>> corrections in the configuration file, and then running everything
>>>>> without
>>>>> skipping steps. This will create all the files that are expected to
>>>>>be
>>>>> there for the registration.
>>>>>
>>>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>>>
>>>>>> Dear Anastasia,
>>>>>>
>>>>>> Thanks for the feedback. So, does this mean that the dcm root should
>>>>>> be
>>>>>> pointed towards the T1¹s? I have the FreeSurfer recon-all output in
>>>>>>a
>>>>>> different folder.
>>>>>> Enclosed is the log file (of one subject) and the configuration
>>>>>>file.
>>>>>> You
>>>>>> will see that I tried the inter and intra option, because I thought
>>>>>> that
>>>>>> for the inter it would not need anything else than the MNI template
>>>>>> and
>>>>>> the DTI images.
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> Best
>>>>>> Heidi
>>>>>>
>>>>>> On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on
>>>>>>behalf
>>>>>> of
>>>>>> Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>>>>> of
>>>>>> ayend...@nmr.mgh.harvard.edu> wrote:
>>>>>>
>>>>>>>
>>>>>>> Hi Heidi - The intra-subject registration step that you're trying
>>>>>>>to
>>>>>>> run
>>>>>>> registers your subject's DWI and T1 images. It expects to find
>>>>>>>those
>>>>>>> images. It doesn't use the FA, MD, etc in any way.
>>>>>>>
>>>>>>> Did the log file get created in scripts/trac-all.log? If so, can
>>>>>>>you
>>>>>>> please send that file and your configuration file? Thanks!
>>>>>>>
>>>>>>> a.y
>>>>>>>
>>>>>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>>>>>
>>>>>>>> Dear FreeSurfers,
>>>>>>>>
>>>>>>>> The data I have is preprocessed, so I have the all the metrics
>>>>>>>>(FA,
>>>>>>>> MD,
>>>>>>>> L1, L2, L3,..) in nifti format.
>>>>>>>> On this data I would like to start tracula starting from step 1.3.
>>>>>>>>
>>>>>>>> I have organized the data as mentioned on the wiki:
>>>>>>>> For example:
>>>>>>>> / dtifit_FA.nii.gz
>>>>>>>>
>>>>>>>> I have also filled in the configuration file, canceling out the
>>>>>>>> things
>>>>>>>> I don¹t need and then I tried to run:
>>>>>>>> Trac-all intra c 
>>>>>>>>
>>>>>>>> Unfortunately, it does not work, it says: dcmlist: subscript out
>>>>>>>>of
>>>>>>>> range
>>>>>>>>
>>>>>>>> I do not have the original filesŠ is there a way that I can get
>>>>>>>>the
>>>>>>>> script working?
>>>>>>>>
>>>>>>>> Many thanks.
>>>>>>>> Heidi
>>>>>>>>
>>>>>>
>>>>
>>


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Re: [Freesurfer] Tracula skip steps

Hmm, weird, as I put a #  in front of it. Putting the eddy current to 0
gives the same error. Enclosed is the config file.
Thank you so much
Heidi

On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ayend...@nmr.mgh.harvard.edu> wrote:

>
>Hi Heidi - It knows where to find the freesurfer recons of the T1's from
>SUBJECTS_DIR (see example config file). Based on your log file, it looks
>like you haven't turned off the eddy current compensation, because it's
>trying to run it. If you attach your config file, I'll take a look.
>
>Best,
>a.y
>
>On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Thanks! I tried to adapt the configuration file and it got a bit
>>further,
>> but then crashes again. Not sure why? I have added the log file, so that
>> maybe you could have a look at what is happening?
>> Also, how does the trac-all command knows where to find the T1 data?
>> Thanks
>> Heidi
>>
>> On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>of
>> Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
>> ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> No, it should be pointed to the DWI data, which can be corrected niftis
>>> instead of the original dicoms. I would recommend turning off all the
>>> corrections in the configuration file, and then running everything
>>> without
>>> skipping steps. This will create all the files that are expected to be
>>> there for the registration.
>>>
>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>
>>>> Dear Anastasia,
>>>>
>>>> Thanks for the feedback. So, does this mean that the dcm root should
>>>>be
>>>> pointed towards the T1¹s? I have the FreeSurfer recon-all output in a
>>>> different folder.
>>>> Enclosed is the log file (of one subject) and the configuration file.
>>>> You
>>>> will see that I tried the inter and intra option, because I thought
>>>>that
>>>> for the inter it would not need anything else than the MNI template
>>>>and
>>>> the DTI images.
>>>>
>>>> Thanks
>>>>
>>>> Best
>>>> Heidi
>>>>
>>>> On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>>> of
>>>> Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>>>of
>>>> ayend...@nmr.mgh.harvard.edu> wrote:
>>>>
>>>>>
>>>>> Hi Heidi - The intra-subject registration step that you're trying to
>>>>> run
>>>>> registers your subject's DWI and T1 images. It expects to find those
>>>>> images. It doesn't use the FA, MD, etc in any way.
>>>>>
>>>>> Did the log file get created in scripts/trac-all.log? If so, can you
>>>>> please send that file and your configuration file? Thanks!
>>>>>
>>>>> a.y
>>>>>
>>>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>>>
>>>>>> Dear FreeSurfers,
>>>>>>
>>>>>> The data I have is preprocessed, so I have the all the metrics (FA,
>>>>>> MD,
>>>>>> L1, L2, L3,..) in nifti format.
>>>>>> On this data I would like to start tracula starting from step 1.3.
>>>>>>
>>>>>> I have organized the data as mentioned on the wiki:
>>>>>> For example:
>>>>>> / dtifit_FA.nii.gz
>>>>>>
>>>>>> I have also filled in the configuration file, canceling out the
>>>>>>things
>>>>>> I don¹t need and then I tried to run:
>>>>>> Trac-all intra c 
>>>>>>
>>>>>> Unfortunately, it does not work, it says: dcmlist: subscript out of
>>>>>> range
>>>>>>
>>>>>> I do not have the original filesŠ is there a way that I can get the
>>>>>> script working?
>>>>>>
>>>>>> Many thanks.
>>>>>> Heidi
>>>>>>
>>>>
>>

#
# dmrirc.example
#
# This file contains commands that will be run by trac-all before an analysis.
# It is used to set all parameters needed for the analysis.
#
# Remove a parameter from your dmrirc file if you want use the default value.
# Parameters that don't

Re: [Freesurfer] Tracula skip steps

Thanks! I tried to adapt the configuration file and it got a bit further,
but then crashes again. Not sure why? I have added the log file, so that
maybe you could have a look at what is happening?
Also, how does the trac-all command knows where to find the T1 data?
Thanks
Heidi

On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ayend...@nmr.mgh.harvard.edu> wrote:

>
>No, it should be pointed to the DWI data, which can be corrected niftis
>instead of the original dicoms. I would recommend turning off all the
>corrections in the configuration file, and then running everything
>without 
>skipping steps. This will create all the files that are expected to be
>there for the registration.
>
>On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Dear Anastasia,
>>
>> Thanks for the feedback. So, does this mean that the dcm root should be
>> pointed towards the T1¹s? I have the FreeSurfer recon-all output in a
>> different folder.
>> Enclosed is the log file (of one subject) and the configuration file.
>>You
>> will see that I tried the inter and intra option, because I thought that
>> for the inter it would not need anything else than the MNI template and
>> the DTI images.
>>
>> Thanks
>>
>> Best
>> Heidi
>>
>> On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>of
>> Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
>> ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> Hi Heidi - The intra-subject registration step that you're trying to
>>>run
>>> registers your subject's DWI and T1 images. It expects to find those
>>> images. It doesn't use the FA, MD, etc in any way.
>>>
>>> Did the log file get created in scripts/trac-all.log? If so, can you
>>> please send that file and your configuration file? Thanks!
>>>
>>> a.y
>>>
>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>
>>>> Dear FreeSurfers,
>>>>
>>>> The data I have is preprocessed, so I have the all the metrics (FA,
>>>>MD,
>>>> L1, L2, L3,..) in nifti format.
>>>> On this data I would like to start tracula starting from step 1.3.
>>>>
>>>> I have organized the data as mentioned on the wiki:
>>>> For example:
>>>> / dtifit_FA.nii.gz
>>>>
>>>> I have also filled in the configuration file, canceling out the things
>>>> I don¹t need and then I tried to run:
>>>> Trac-all intra c 
>>>>
>>>> Unfortunately, it does not work, it says: dcmlist: subscript out of
>>>> range
>>>>
>>>> I do not have the original filesŠ is there a way that I can get the
>>>> script working?
>>>>
>>>> Many thanks.
>>>> Heidi
>>>>
>>



dwi.ecclog
Description: dwi.ecclog


trac-all.log
Description: trac-all.log
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Re: [Freesurfer] Tracula skip steps

Dear Anastasia,

Thanks for the feedback. So, does this mean that the dcm root should be
pointed towards the T1¹s? I have the FreeSurfer recon-all output in a
different folder.
Enclosed is the log file (of one subject) and the configuration file. You
will see that I tried the inter and intra option, because I thought that
for the inter it would not need anything else than the MNI template and
the DTI images.

Thanks

Best
Heidi

On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ayend...@nmr.mgh.harvard.edu> wrote:

>
>Hi Heidi - The intra-subject registration step that you're trying to run
>registers your subject's DWI and T1 images. It expects to find those
>images. It doesn't use the FA, MD, etc in any way.
>
>Did the log file get created in scripts/trac-all.log? If so, can you
>please send that file and your configuration file? Thanks!
>
>a.y
>
>On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Dear FreeSurfers,
>> 
>> The data I have is preprocessed, so I have the all the metrics (FA, MD,
>>L1, L2, L3,..) in nifti format.
>> On this data I would like to start tracula starting from step 1.3.
>> 
>> I have organized the data as mentioned on the wiki:
>> For example:
>> / dtifit_FA.nii.gz
>> 
>> I have also filled in the configuration file, canceling out the things
>>I don¹t need and then I tried to run:
>> Trac-all intra c 
>> 
>> Unfortunately, it does not work, it says: dcmlist: subscript out of
>>range
>> 
>> I do not have the original filesŠ is there a way that I can get the
>>script working?
>> 
>> Many thanks.
>> Heidi
>> 

#
# dmrirc.example
#
# This file contains commands that will be run by trac-all before an analysis.
# It is used to set all parameters needed for the analysis.
#
# Remove a parameter from your dmrirc file if you want use the default value.
# Parameters that don't have default values must be specified.
#
# Any other commands that you might want to run before an analysis can be added
# to this file.
#
# Original Author: Anastasia Yendiki
# CVS Revision Info:
#$Author: ayendiki $
#$Date: 2013/12/05 23:08:54 $
#$Revision: 1.12 $
#
# Copyright Â© 2011 The General Hospital Corporation (Boston, MA) "MGH"
#
# Terms and conditions for use, reproduction, distribution and contribution
# are found in the 'FreeSurfer Software License Agreement' contained
# in the file 'LICENSE' found in the FreeSurfer distribution, and here:
#
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
#
# Reporting: freesurfer@nmr.mgh.harvard.edu
#
#

# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
# 
#setenv SUBJECTS_DIR /path/to/recons/of/ducks
#
# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = /Volumes/MACPRO1/EXPLORE_DTI_analyses/dtifit/

# Subject IDs
#
set subjlist = ` echo S_11XDXA S_1GQ9QV S_1OR6QC S_22ZHN3 S_2AL8RA S_2BB4H2 
S_2C71QF S_2N88VA S_38ZNK5 S_3RSPPP S_3VZEQN S_46JBNZ S_4MPQCY S_4WJ2CR 
S_556CFT S_591HTP S_5KA3RS S_65UK1S S_693X4P S_6D51EY S_6FWKZD S_6FZL4U 
S_6SB9KZ S_6YRT6A S_71GPF7 S_7HSOBN S_7KFHPW S_7NOX7M S_7WP6BG S_82FZ4L 
S_8BWFJ6 S_9737MM S_9EUNFD S_9K8SLX S_9N8KQW S_9P3JR7 S_9ZVDZV S_A1F2CM 
S_ALV5CB S_AUL7R4 S_BZ4FBH S_CCCMW3 S_CMM2WL S_CTY2ER S_CU4FZA S_CURLLB 
S_DL4N2Q S_DNQ9KU S_DQ1ZSG S_DTW7J6 S_DWA2LP S_DXM9JK S_EHDWX1 S_ENG47C 
S_F4PH5M S_F8P42D S_FCBAMR S_FDJ6UU S_FMSJER S_FQHJWH S_FSK1HD S_FWFNC5 
S_G7KP27 S_H7YAA1 S_HCFNSF S_HW7R19 S_HWGXLJ S_J9HY8A S_JY5M58 S_K1K5LS 
S_K8ZC3B S_KBGJQU S_KCT9S6 S_KL5Q3P S_KMUW5L S_L33YSL S_LABYUQ S_LJ1GWN 
S_LLPPCW S_MEEDAH S_MFUFDS S_MX83QU S_NE58SM S_NIQUVD S_P4K6DM S_PE9J6U 
S_Q9A2UG S_QS6SFY S_R3BPAK S_RANV43 S_RFDRD6 S_RHXWND S_SO63PR S_SVAQUY 
S_T1LVDV S_T8CBM1 S_TJIU8X S_TMNXYB S_TNS7IM S_U2V5FD S_U98RJE S_U9U9QL 
S_UHC6WM S_V36DLL S_VTMXMZ S_WA1CLD S_WDVBAY S_X69RWA S_XFNM9K S_XRZQKV 
S_XTDEMR S_XXMGFN S_XY62WP S_Y97L76 S_YANQMX S_YEFGQ2 S_ZASXXZ S_ZNUP4E 
S_ZPBHLL TAU_001 TAU_024 TAU_029 TAU_064 TAU_074 TAU_122 TAU_151 TAU_154 
TAU_156 TAU_157 TAU_160 TAU_161 TAU_169 TAU_175 TAU_178 TAU_180`

# In case you want to analyze only Huey and Louie
# Default: Run analysis on all subjects
#
#set runlist = (1 3)
#
# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then the gradient table and b-value table must be specified (see below)
#
#set dcmroot = /Volumes/MACPRO1/EXPLORE_DTI_analyses/prep/
#set dcmlist = (huey/day1/XXX-1.dcm dewey/day1/XXX-1.dcm louie/day2/XXX-1.dcm)

# Diffusion gradient tables (if there is a different one for each scan)
# Must be specified if inputs are not MGH DICOMs
# The tables must have either three columns, whe

[Freesurfer] Tracula skip steps

2016-05-30 Thread Jacobs H (NP)

Dear FreeSurfers,

The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, 
L3,..) in nifti format.
On this data I would like to start tracula starting from step 1.3.

I have organized the data as mentioned on the wiki:
For example:
/ dtifit_FA.nii.gz

I have also filled in the configuration file, canceling out the things I don't 
need and then I tried to run:
Trac-all -intra -c 

Unfortunately, it does not work, it says: dcmlist: subscript out of range

I do not have the original files... is there a way that I can get the script 
working?

Many thanks.
Heidi
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[Freesurfer] amygdala nuclear subregions

2016-01-08 Thread Jacobs H (NP)

Dear FreeSurfer developers,

In the FreeSurferColorLut file I see labels for the subregions of the amygdala.
Is it possible to extract the volumes for these regions? And how can I do this? 
I don't see them in the aseg or aparc stat files.

Many thanks!
Heidi
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Re: [Freesurfer] changing the index of labels

2015-11-04 Thread Jacobs H (NP)

Works perfectly! Thank you so much!
Heidi

On 11/3/15, 6:54 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote:

>
>In that case you can do something like
>fscalc lhfile.mgz add 1000 -o lhfile1000.mgz
>mri_mask lhfile1000.mgz lhfile.mgz lhfile1000.mgz
>
>This will add 1000 to the lhlabels. This will make the lh labels
>different from the rh. You can add a constant to the rh too if you want.
>
>doug
>
>
>On 10/30/2015 07:12 PM, Jacobs H (NP) wrote:
>> Yes, there are different mgz files for left and right (but they have the
>> same index numbers and colors).
>>
>> On 10/30/15, 11:16 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>wrote:
>>
>>> Are there different files for the lh and rh? Sorry, never done the
>>> subfields analysis.
>>>
>>>
>>> On 10/30/2015 01:25 PM, Bruce Fischl wrote:
>>>> Hi Heidi
>>>>
>>>> I guess you could do it yourself in matlab using the aseg to figure
>>>> out which hemisphere you are in
>>>>
>>>> cheers
>>>> Bruce
>>>>
>>>> On Fri, 30 Oct 2015, Jacobs H (NP) wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> Is there a way to change the index of the segmentation of the
>>>>> hippocampal
>>>>> subfields, so that when I combine left and right, FreeSurfer treats
>>>>> them
>>>>> as different regions?
>>>>>
>>>>> Thanks!
>>>>> Best
>>>>> Heidi
>>>>>
>>>>>>> I just checked again in freeview and indeed they have the same
>>>>>>>index
>>>>>>> (e.g.
>>>>>>> CA1 has value 206 for left and also for right).
>>>>>>>
>>>>>>> On 10/27/15, 5:01 PM, "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> The color is not important. The question is whether they have a
>>>>>>>> different index. Can you confirm that lh and rh have the same
>>>>>>>>index?
>>>>>>>>
>>>>>>>> On 10/27/15 11:53 AM, Jacobs H (NP) wrote:
>>>>>>>>> Hi Doug,
>>>>>>>>>
>>>>>>>>> Yes, for the aseg they are. But not for the hippocampal
>>>>>>>>>subfields:
>>>>>>>>> left
>>>>>>>>> and right have the same color coding.
>>>>>>>>> I am creating one segmentation, including left and right
>>>>>>>>> hippocampal
>>>>>>>>> subfields and aparc, for partial volume correction.
>>>>>>>>> Any idea how I can make the labels for the hippocampal subfields
>>>>>>>>> different
>>>>>>>>> (freesurfer version 6)?
>>>>>>>>>
>>>>>>>>> Thanks
>>>>>>>>> Heidi
>>>>>>>>>
>>>>>>>>> On 10/27/15, 4:32 PM, "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> The indices should be different. Eg, 17 is left hippo, 53 is
>>>>>>>>>>right
>>>>>>>>>> hippo. If you click on them in freeview and different labels
>>>>>>>>>> appear,
>>>>>>>>>> then FS knows they are different
>>>>>>>>>>
>>>>>>>>>> On 10/24/15 9:29 PM, Jacobs H (NP) wrote:
>>>>>>>>>>> Hi.
>>>>>>>>>>>
>>>>>>>>>>> Just one another related question: now that I was able to
>>>>>>>>>>>combine
>>>>>>>>>>> left
>>>>>>>>>>> and
>>>>>>>>>>> right hippocampal subfields with the aparc-aseg correctly, I
>>>>>>>>>>> noticed
>>>>>>>>>>> that
>>>>>>>>>>> the left and right hippocampal subfields have the same color
>>>>>>>>>>> labels
>>>>>>>>>>> and
>>>>>>>>>>> codes. What

Re: [Freesurfer] changing the index of labels

2015-10-30 Thread Jacobs H (NP)

Yes, there are different mgz files for left and right (but they have the
same index numbers and colors).

On 10/30/15, 11:16 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote:

>
>Are there different files for the lh and rh? Sorry, never done the
>subfields analysis.
>
>
>On 10/30/2015 01:25 PM, Bruce Fischl wrote:
>> Hi Heidi
>>
>> I guess you could do it yourself in matlab using the aseg to figure
>> out which hemisphere you are in
>>
>> cheers
>> Bruce
>>
>> On Fri, 30 Oct 2015, Jacobs H (NP) wrote:
>>
>>>
>>> Hi,
>>>
>>> Is there a way to change the index of the segmentation of the
>>> hippocampal
>>> subfields, so that when I combine left and right, FreeSurfer treats
>>>them
>>> as different regions?
>>>
>>> Thanks!
>>> Best
>>> Heidi
>>>
>>>>
>>>>> I just checked again in freeview and indeed they have the same index
>>>>> (e.g.
>>>>> CA1 has value 206 for left and also for right).
>>>>>
>>>>> On 10/27/15, 5:01 PM, "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
>>>>> wrote:
>>>>>
>>>>>> The color is not important. The question is whether they have a
>>>>>> different index. Can you confirm that lh and rh have the same index?
>>>>>>
>>>>>> On 10/27/15 11:53 AM, Jacobs H (NP) wrote:
>>>>>>> Hi Doug,
>>>>>>>
>>>>>>> Yes, for the aseg they are. But not for the hippocampal subfields:
>>>>>>> left
>>>>>>> and right have the same color coding.
>>>>>>> I am creating one segmentation, including left and right
>>>>>>>hippocampal
>>>>>>> subfields and aparc, for partial volume correction.
>>>>>>> Any idea how I can make the labels for the hippocampal subfields
>>>>>>> different
>>>>>>> (freesurfer version 6)?
>>>>>>>
>>>>>>> Thanks
>>>>>>> Heidi
>>>>>>>
>>>>>>> On 10/27/15, 4:32 PM, "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> The indices should be different. Eg, 17 is left hippo, 53 is right
>>>>>>>> hippo. If you click on them in freeview and different labels
>>>>>>>> appear,
>>>>>>>> then FS knows they are different
>>>>>>>>
>>>>>>>> On 10/24/15 9:29 PM, Jacobs H (NP) wrote:
>>>>>>>>> Hi.
>>>>>>>>>
>>>>>>>>> Just one another related question: now that I was able to combine
>>>>>>>>> left
>>>>>>>>> and
>>>>>>>>> right hippocampal subfields with the aparc-aseg correctly, I
>>>>>>>>> noticed
>>>>>>>>> that
>>>>>>>>> the left and right hippocampal subfields have the same color
>>>>>>>>> labels
>>>>>>>>> and
>>>>>>>>> codes. What would be the best way to make sure that FreeSurfer
>>>>>>>>> understand
>>>>>>>>> that the left and right subfields (e.g. Left and right CA1) are
>>>>>>>>> different
>>>>>>>>> areas?
>>>>>>>>>
>>>>>>>>> Thanks!
>>>>>>>>> Heidi
>>>>>>>>>
>>>>>>>>> On 10/21/15, 11:01 PM, "Jacobs H (NP)"
>>>>>>>>> <h.jac...@maastrichtuniversity.nl>
>>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>>> Thanks! Works wonderful!
>>>>>>>>>> Heidi
>>>>>>>>>>
>>>>>>>>>> On 10/21/15, 10:50 PM, "Douglas N Greve"
>>>>>>>>>> <gr...@nmr.mgh.harvard.edu>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>> If you want to remove them, you can use mri_binarize with the
>>>>>>>>>>> --replace
>>>>>>>>>>> option

[Freesurfer] changing the index of labels

2015-10-30 Thread Jacobs H (NP)


Hi,

Is there a way to change the index of the segmentation of the hippocampal
subfields, so that when I combine left and right, FreeSurfer treats them
as different regions?

Thanks!
Best
Heidi

>
>>I just checked again in freeview and indeed they have the same index
>>(e.g.
>>CA1 has value 206 for left and also for right).
>>
>>On 10/27/15, 5:01 PM, "Douglas Greve" <gr...@nmr.mgh.harvard.edu> wrote:
>>
>>>The color is not important. The question is whether they have a
>>>different index. Can you confirm that lh and rh have the same index?
>>>
>>>On 10/27/15 11:53 AM, Jacobs H (NP) wrote:
>>>> Hi Doug,
>>>>
>>>> Yes, for the aseg they are. But not for the hippocampal subfields:
>>>>left
>>>> and right have the same color coding.
>>>> I am creating one segmentation, including left and right hippocampal
>>>> subfields and aparc, for partial volume correction.
>>>> Any idea how I can make the labels for the hippocampal subfields
>>>>different
>>>> (freesurfer version 6)?
>>>>
>>>> Thanks
>>>> Heidi
>>>>
>>>> On 10/27/15, 4:32 PM, "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
>>>>wrote:
>>>>
>>>>> The indices should be different. Eg, 17 is left hippo, 53 is right
>>>>> hippo. If you click on them in freeview and different labels appear,
>>>>> then FS knows they are different
>>>>>
>>>>> On 10/24/15 9:29 PM, Jacobs H (NP) wrote:
>>>>>> Hi.
>>>>>>
>>>>>> Just one another related question: now that I was able to combine
>>>>>>left
>>>>>> and
>>>>>> right hippocampal subfields with the aparc-aseg correctly, I noticed
>>>>>> that
>>>>>> the left and right hippocampal subfields have the same color labels
>>>>>>and
>>>>>> codes. What would be the best way to make sure that FreeSurfer
>>>>>> understand
>>>>>> that the left and right subfields (e.g. Left and right CA1) are
>>>>>> different
>>>>>> areas? 
>>>>>>
>>>>>> Thanks!
>>>>>> Heidi
>>>>>>
>>>>>> On 10/21/15, 11:01 PM, "Jacobs H (NP)"
>>>>>> <h.jac...@maastrichtuniversity.nl>
>>>>>> wrote:
>>>>>>
>>>>>>> Thanks! Works wonderful!
>>>>>>> Heidi
>>>>>>>
>>>>>>> On 10/21/15, 10:50 PM, "Douglas N Greve"
>>>>>>><gr...@nmr.mgh.harvard.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> If you want to remove them, you can use mri_binarize with the
>>>>>>>> --replace
>>>>>>>> option, replacing them with whatever you want.
>>>>>>>>
>>>>>>>> On 10/21/2015 04:38 PM, Jacobs H (NP) wrote:
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> I am trying to generate a segmentation file containing the
>>>>>>>>>aseg+aparc
>>>>>>>>> but replacing the hippocampus with the hippocampal subfields.
>>>>>>>>> With mergeseg I was able to merge the segmentations, but
>>>>>>>>> unfortunately
>>>>>>>>> parts of the ³old² hippocampus (labeled as 17 and 53) are still
>>>>>>>>>in
>>>>>>>>> there (as the area covered by the subfields is not 100% equal to
>>>>>>>>>the
>>>>>>>>> hippocampus of the aseg).
>>>>>>>>> How can I remove the remains of the old hippocampal labels?
>>>>>>>>>
>>>>>>>>> Many thanks!
>>>>>>>>> Best
>>>>>>>>> Heidi
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ___
>>>>>>>>> Freesurfer mailing list
>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>>> -- 
>>>>>>>> Douglas N. Greve

Re: [Freesurfer] remove label from aseg

2015-10-28 Thread Jacobs H (NP)

I think this one thread might have disappeared (if not, I apologize for my
impatience).
Heidi

On 10/27/15, 5:16 PM, "Jacobs H (NP)" <h.jac...@maastrichtuniversity.nl>
wrote:

>I just checked again in freeview and indeed they have the same index (e.g.
>CA1 has value 206 for left and also for right).
>
>On 10/27/15, 5:01 PM, "Douglas Greve" <gr...@nmr.mgh.harvard.edu> wrote:
>
>>The color is not important. The question is whether they have a
>>different index. Can you confirm that lh and rh have the same index?
>>
>>On 10/27/15 11:53 AM, Jacobs H (NP) wrote:
>>> Hi Doug,
>>>
>>> Yes, for the aseg they are. But not for the hippocampal subfields: left
>>> and right have the same color coding.
>>> I am creating one segmentation, including left and right hippocampal
>>> subfields and aparc, for partial volume correction.
>>> Any idea how I can make the labels for the hippocampal subfields
>>>different
>>> (freesurfer version 6)?
>>>
>>> Thanks
>>> Heidi
>>>
>>> On 10/27/15, 4:32 PM, "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
>>>wrote:
>>>
>>>> The indices should be different. Eg, 17 is left hippo, 53 is right
>>>> hippo. If you click on them in freeview and different labels appear,
>>>> then FS knows they are different
>>>>
>>>> On 10/24/15 9:29 PM, Jacobs H (NP) wrote:
>>>>> Hi.
>>>>>
>>>>> Just one another related question: now that I was able to combine
>>>>>left
>>>>> and
>>>>> right hippocampal subfields with the aparc-aseg correctly, I noticed
>>>>> that
>>>>> the left and right hippocampal subfields have the same color labels
>>>>>and
>>>>> codes. What would be the best way to make sure that FreeSurfer
>>>>> understand
>>>>> that the left and right subfields (e.g. Left and right CA1) are
>>>>> different
>>>>> areas? 
>>>>>
>>>>> Thanks!
>>>>> Heidi
>>>>>
>>>>> On 10/21/15, 11:01 PM, "Jacobs H (NP)"
>>>>> <h.jac...@maastrichtuniversity.nl>
>>>>> wrote:
>>>>>
>>>>>> Thanks! Works wonderful!
>>>>>> Heidi
>>>>>>
>>>>>> On 10/21/15, 10:50 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>>>>> wrote:
>>>>>>
>>>>>>> If you want to remove them, you can use mri_binarize with the
>>>>>>> --replace
>>>>>>> option, replacing them with whatever you want.
>>>>>>>
>>>>>>> On 10/21/2015 04:38 PM, Jacobs H (NP) wrote:
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I am trying to generate a segmentation file containing the
>>>>>>>>aseg+aparc
>>>>>>>> but replacing the hippocampus with the hippocampal subfields.
>>>>>>>> With mergeseg I was able to merge the segmentations, but
>>>>>>>> unfortunately
>>>>>>>> parts of the ³old² hippocampus (labeled as 17 and 53) are still in
>>>>>>>> there (as the area covered by the subfields is not 100% equal to
>>>>>>>>the
>>>>>>>> hippocampus of the aseg).
>>>>>>>> How can I remove the remains of the old hippocampal labels?
>>>>>>>>
>>>>>>>> Many thanks!
>>>>>>>> Best
>>>>>>>> Heidi
>>>>>>>>
>>>>>>>>
>>>>>>>> ___
>>>>>>>> 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/fi

Re: [Freesurfer] remove label from aseg

2015-10-27 Thread Jacobs H (NP)

Hi Doug,

Yes, for the aseg they are. But not for the hippocampal subfields: left
and right have the same color coding.
I am creating one segmentation, including left and right hippocampal
subfields and aparc, for partial volume correction.
Any idea how I can make the labels for the hippocampal subfields different
(freesurfer version 6)?

Thanks
Heidi

On 10/27/15, 4:32 PM, "Douglas Greve" <gr...@nmr.mgh.harvard.edu> wrote:

>The indices should be different. Eg, 17 is left hippo, 53 is right
>hippo. If you click on them in freeview and different labels appear,
>then FS knows they are different
>
>On 10/24/15 9:29 PM, Jacobs H (NP) wrote:
>> Hi.
>>
>> Just one another related question: now that I was able to combine left
>>and
>> right hippocampal subfields with the aparc-aseg correctly, I noticed
>>that
>> the left and right hippocampal subfields have the same color labels and
>> codes. What would be the best way to make sure that FreeSurfer
>>understand
>> that the left and right subfields (e.g. Left and right CA1) are
>>different
>> areas? 
>>
>> Thanks!
>> Heidi
>>
>> On 10/21/15, 11:01 PM, "Jacobs H (NP)"
>><h.jac...@maastrichtuniversity.nl>
>> wrote:
>>
>>> Thanks! Works wonderful!
>>> Heidi
>>>
>>> On 10/21/15, 10:50 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>> wrote:
>>>
>>>> If you want to remove them, you can use mri_binarize with the
>>>>--replace
>>>> option, replacing them with whatever you want.
>>>>
>>>> On 10/21/2015 04:38 PM, Jacobs H (NP) wrote:
>>>>> Hi,
>>>>>
>>>>> I am trying to generate a segmentation file containing the aseg+aparc
>>>>> but replacing the hippocampus with the hippocampal subfields.
>>>>> With mergeseg I was able to merge the segmentations, but
>>>>>unfortunately
>>>>> parts of the ³old² hippocampus (labeled as 17 and 53) are still in
>>>>> there (as the area covered by the subfields is not 100% equal to the
>>>>> hippocampus of the aseg).
>>>>> How can I remove the remains of the old hippocampal labels?
>>>>>
>>>>> Many thanks!
>>>>> Best
>>>>> Heidi
>>>>>
>>>>>
>>>>> ___
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>> -- 
>>>> Douglas N. Greve, Ph.D.
>>>> MGH-NMR Center
>>>> gr...@nmr.mgh.harvard.edu
>>>> Phone Number: 617-724-2358
>>>> Fax: 617-726-7422
>>>>
>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>>> Outgoing: 
>>>>ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>>
>>>> ___
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>> The information in this e-mail is intended only for the person to
>>>>whom it
>>>> is
>>>> addressed. If you believe this e-mail was sent to you in error and the
>>>> e-mail
>>>> contains patient information, please contact the Partners Compliance
>>>> HelpLine at
>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>you in
>>>> error
>>>> but does not contain patient information, please contact the sender
>>>>and
>>>> properly
>>>> dispose of the e-mail.
>>>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
>___
>Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] remove label from aseg

2015-10-27 Thread Jacobs H (NP)

I just checked again in freeview and indeed they have the same index (e.g.
CA1 has value 206 for left and also for right).

On 10/27/15, 5:01 PM, "Douglas Greve" <gr...@nmr.mgh.harvard.edu> wrote:

>The color is not important. The question is whether they have a
>different index. Can you confirm that lh and rh have the same index?
>
>On 10/27/15 11:53 AM, Jacobs H (NP) wrote:
>> Hi Doug,
>>
>> Yes, for the aseg they are. But not for the hippocampal subfields: left
>> and right have the same color coding.
>> I am creating one segmentation, including left and right hippocampal
>> subfields and aparc, for partial volume correction.
>> Any idea how I can make the labels for the hippocampal subfields
>>different
>> (freesurfer version 6)?
>>
>> Thanks
>> Heidi
>>
>> On 10/27/15, 4:32 PM, "Douglas Greve" <gr...@nmr.mgh.harvard.edu> wrote:
>>
>>> The indices should be different. Eg, 17 is left hippo, 53 is right
>>> hippo. If you click on them in freeview and different labels appear,
>>> then FS knows they are different
>>>
>>> On 10/24/15 9:29 PM, Jacobs H (NP) wrote:
>>>> Hi.
>>>>
>>>> Just one another related question: now that I was able to combine left
>>>> and
>>>> right hippocampal subfields with the aparc-aseg correctly, I noticed
>>>> that
>>>> the left and right hippocampal subfields have the same color labels
>>>>and
>>>> codes. What would be the best way to make sure that FreeSurfer
>>>> understand
>>>> that the left and right subfields (e.g. Left and right CA1) are
>>>> different
>>>> areas? 
>>>>
>>>> Thanks!
>>>> Heidi
>>>>
>>>> On 10/21/15, 11:01 PM, "Jacobs H (NP)"
>>>> <h.jac...@maastrichtuniversity.nl>
>>>> wrote:
>>>>
>>>>> Thanks! Works wonderful!
>>>>> Heidi
>>>>>
>>>>> On 10/21/15, 10:50 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>>>> wrote:
>>>>>
>>>>>> If you want to remove them, you can use mri_binarize with the
>>>>>> --replace
>>>>>> option, replacing them with whatever you want.
>>>>>>
>>>>>> On 10/21/2015 04:38 PM, Jacobs H (NP) wrote:
>>>>>>> Hi,
>>>>>>>
>>>>>>> I am trying to generate a segmentation file containing the
>>>>>>>aseg+aparc
>>>>>>> but replacing the hippocampus with the hippocampal subfields.
>>>>>>> With mergeseg I was able to merge the segmentations, but
>>>>>>> unfortunately
>>>>>>> parts of the ³old² hippocampus (labeled as 17 and 53) are still in
>>>>>>> there (as the area covered by the subfields is not 100% equal to
>>>>>>>the
>>>>>>> hippocampus of the aseg).
>>>>>>> How can I remove the remains of the old hippocampal labels?
>>>>>>>
>>>>>>> Many thanks!
>>>>>>> Best
>>>>>>> Heidi
>>>>>>>
>>>>>>>
>>>>>>> ___
>>>>>>> Freesurfer mailing list
>>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>> -- 
>>>>>> Douglas N. Greve, Ph.D.
>>>>>> MGH-NMR Center
>>>>>> gr...@nmr.mgh.harvard.edu
>>>>>> Phone Number: 617-724-2358
>>>>>> Fax: 617-726-7422
>>>>>>
>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>>>>> Outgoing: 
>>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>>>>
>>>>>> ___
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>>
>>>>>> The information in this e-mail is intended only for the person to
>>>>>> whom it
>>>>>> is
>>>>>> addressed. If you believe this e-mail was sent to you in error and
>>>>>>the
>>>>>> e-mail
>>>>>> contains patient information, please contact the Partners Compliance
>>>>>> HelpLine at
>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>>> you in
>>>>>> error
>>>>>> but does not contain patient information, please contact the sender
>>>>>> and
>>>>>> properly
>>>>>> dispose of the e-mail.
>>>>>>
>>>> ___
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>> ___
>>> 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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>Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] : FOLLOW-UP question: remove label from aseg

2015-10-26 Thread Jacobs H (NP)



On 10/25/15, 3:29 AM, "Jacobs H (NP)" <h.jac...@maastrichtuniversity.nl>
wrote:

>Hi.
>
>Just one another related question: now that I was able to combine left and
>right hippocampal subfields with the aparc-aseg correctly, I noticed that
>the left and right hippocampal subfields have the same color labels and
>codes. What would be the best way to make sure that FreeSurfer understand
>that the left and right subfields (e.g. Left and right CA1) are different
>areas? 
>
>Thanks!
>Heidi
>
>On 10/21/15, 11:01 PM, "Jacobs H (NP)" <h.jac...@maastrichtuniversity.nl>
>wrote:
>
>>Thanks! Works wonderful!
>>Heidi
>>
>>On 10/21/15, 10:50 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>wrote:
>>
>>>If you want to remove them, you can use mri_binarize with the --replace
>>>option, replacing them with whatever you want.
>>>
>>>On 10/21/2015 04:38 PM, Jacobs H (NP) wrote:
>>>> Hi,
>>>>
>>>> I am trying to generate a segmentation file containing the aseg+aparc
>>>> but replacing the hippocampus with the hippocampal subfields.
>>>> With mergeseg I was able to merge the segmentations, but unfortunately
>>>> parts of the ³old² hippocampus (labeled as 17 and 53) are still in
>>>> there (as the area covered by the subfields is not 100% equal to the
>>>> hippocampus of the aseg).
>>>> How can I remove the remains of the old hippocampal labels?
>>>>
>>>> Many thanks!
>>>> Best
>>>> Heidi
>>>>
>>>>
>>>> ___
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>-- 
>>>Douglas N. Greve, Ph.D.
>>>MGH-NMR Center
>>>gr...@nmr.mgh.harvard.edu
>>>Phone Number: 617-724-2358
>>>Fax: 617-726-7422
>>>
>>>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>>www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>>Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
>>>___
>>>Freesurfer mailing list
>>>Freesurfer@nmr.mgh.harvard.edu
>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>The information in this e-mail is intended only for the person to whom
>>>it
>>>is
>>>addressed. If you believe this e-mail was sent to you in error and the
>>>e-mail
>>>contains patient information, please contact the Partners Compliance
>>>HelpLine at
>>>http://www.partners.org/complianceline . If the e-mail was sent to you
>>>in
>>>error
>>>but does not contain patient information, please contact the sender and
>>>properly
>>>dispose of the e-mail.
>>>
>>
>


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[Freesurfer] remove label from aseg

2015-10-21 Thread Jacobs H (NP)

Hi,

I am trying to generate a segmentation file containing the aseg+aparc but 
replacing the hippocampus with the hippocampal subfields.
With mergeseg I was able to merge the segmentations, but unfortunately parts of 
the “old” hippocampus (labeled as 17 and 53) are still in there (as the area 
covered by the subfields is not 100% equal to the hippocampus of the aseg).
How can I remove the remains of the old hippocampal labels?

Many thanks!
Best
Heidi
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] remove label from aseg

2015-10-21 Thread Jacobs H (NP)

Thanks! Works wonderful!
Heidi

On 10/21/15, 10:50 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote:

>If you want to remove them, you can use mri_binarize with the --replace
>option, replacing them with whatever you want.
>
>On 10/21/2015 04:38 PM, Jacobs H (NP) wrote:
>> Hi,
>>
>> I am trying to generate a segmentation file containing the aseg+aparc
>> but replacing the hippocampus with the hippocampal subfields.
>> With mergeseg I was able to merge the segmentations, but unfortunately
>> parts of the ³old² hippocampus (labeled as 17 and 53) are still in
>> there (as the area covered by the subfields is not 100% equal to the
>> hippocampus of the aseg).
>> How can I remove the remains of the old hippocampal labels?
>>
>> Many thanks!
>> Best
>> Heidi
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>-- 
>Douglas N. Greve, Ph.D.
>MGH-NMR Center
>gr...@nmr.mgh.harvard.edu
>Phone Number: 617-724-2358
>Fax: 617-726-7422
>
>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>The information in this e-mail is intended only for the person to whom it
>is
>addressed. If you believe this e-mail was sent to you in error and the
>e-mail
>contains patient information, please contact the Partners Compliance
>HelpLine at
>http://www.partners.org/complianceline . If the e-mail was sent to you in
>error
>but does not contain patient information, please contact the sender and
>properly
>dispose of the e-mail.
>


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Re: [Freesurfer] warping surface label to volume space

2015-10-02 Thread Jacobs H (NP)

Hi Doug,

Thanks for checking the data!
I just removed the output volume, ran the command again and got the same
weird output.
Since it worked for you, I tried it again… no change.
However, then I noticed that the mri_vol2label uses the SUBJECTS_DIR path
and this was not set to this folder (I was trying some things out in a
temporary folder). So, probably, it was using data from the subject in the
original SUBJECTS_DIR folder? I changed that and the output looks
beautiful now! It is kind of weird, as the original SUBJECTS_DIR was done
in the same version.

But it is working beautifully now!!! Thank you so much for your help!
Best
Heidi



On 02/10/15 20:57, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote:

>I'm at a loss here. I run the exact same command with the same version.
>I get the same terminal output, but my output volume looks ok. The only
>thing I can think of is that there is an old version that output volume
>that is not getting overwritten. Can you name the output file
>differently and make sure that it does not exist prior to running the
>command?
>
>On 09/30/2015 04:37 PM, Jacobs H (NP) wrote:
>> Hi Doug,
>>
>> Just as a reminder: I uploaded the data yesterday.
>>
>> Best
>> Heidi
>>
>> From: Douglas Greve <gr...@nmr.mgh.harvard.edu
>> <mailto:gr...@nmr.mgh.harvard.edu>>
>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
>> <mailto:freesurfer@nmr.mgh.harvard.edu>>
>> Date: Tuesday 29 September 2015 17:01
>> To: "freesurfer@nmr.mgh.harvard.edu
>> <mailto:freesurfer@nmr.mgh.harvard.edu>"
>> <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>
>> Subject: Re: [Freesurfer] warping surface label to volume space
>>
>> filedrop2 url at the end of this email
>>
>> On 9/29/15 10:34 AM, Jacobs H (NP) wrote:
>>> Sure, where should I upload it to?
>>> Thanks!
>>> Heidi
>>>
>>> From: Douglas Greve <gr...@nmr.mgh.harvard.edu
>>> <mailto:gr...@nmr.mgh.harvard.edu>>
>>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
>>> <mailto:freesurfer@nmr.mgh.harvard.edu>>
>>> Date: Tuesday 29 September 2015 16:28
>>> To: "freesurfer@nmr.mgh.harvard.edu
>>> <mailto:freesurfer@nmr.mgh.harvard.edu>"
>>> <freesurfer@nmr.mgh.harvard.edu
>>><mailto:freesurfer@nmr.mgh.harvard.edu>>
>>> Subject: Re: [Freesurfer] warping surface label to volume space
>>>
>>> Can you upload the subject so I can look at it?
>>>
>>> On 9/29/15 9:05 AM, Jacobs H (NP) wrote:
>>>> Hi Doug,
>>>>
>>>> The label looks actually ok and the surface as well. I attached the
>>>>images to this email, Not sure where it went wrong?
>>>>
>>>> Best
>>>> Heidi
>>>>
>>>> 
>>>> Van:freesurfer-boun...@nmr.mgh.harvard.edu
>>>>[freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve
>>>>[gr...@nmr.mgh.harvard.edu]
>>>> Verzonden: maandag 28 september 2015 23:58
>>>> Aan:freesurfer@nmr.mgh.harvard.edu
>>>> Onderwerp: Re: [Freesurfer] warping surface label to volume space
>>>>
>>>> Something is definitely going wrong. Can you load the label as well
>>>>and
>>>> verify that the label itself looks ok?
>>>>
>>>> On 09/28/2015 05:32 PM, Jacobs H (NP) wrote:
>>>>> Yes, here it is!
>>>>> Thanks! Heidi
>>>>>
>>>>>
>>>>>
>>>>> Yes, here it is!
>>>>> Thanks! Heidi
>>>>>
>>>>>
>>>>> image1.png
>>>>>
>>>>>
>>>>>
>>>>> ATT1.txt
>>>>>
>>>>>
>>>>>
>>>>>> Op 28 sep. 2015 om 17:26 heeft Douglas N
>>>>>>Greve<gr...@nmr.mgh.harvard.edu>   het volgende geschreven:
>>>>>>
>>>>>> Can you send a picture?
>>>>>>
>>>>>>> On 09/28/2015 05:08 PM, Jacobs H (NP) wrote:
>>>>>>> Dear Doug,
>>>>>>>
>>>>>>> By looking at it in Freeview. Anatomically, I would expect that
>>>>>>>the entorhinal cortex would not be localized so laterally? And some
>>>>>>>voxels are not in the temporal lobe.
>>>>>>>
>>>>>>>

Re: [Freesurfer] warping surface label to volume space

2015-10-01 Thread Jacobs H (NP)

Hi Doug,

Just as a reminder: I uploaded the data yesterday.

Best
Heidi

From: Douglas Greve 
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>>
Reply-To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday 29 September 2015 17:01
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] warping surface label to volume space

filedrop2 url at the end of this email

On 9/29/15 10:34 AM, Jacobs H (NP) wrote:
Sure, where should I upload it to?
Thanks!
Heidi

From: Douglas Greve 
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>>
Reply-To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday 29 September 2015 16:28
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] warping surface label to volume space

Can you upload the subject so I can look at it?

On 9/29/15 9:05 AM, Jacobs H (NP) wrote:

Hi Doug,

The label looks actually ok and the surface as well. I attached the images to 
this email, Not sure where it went wrong?

Best
Heidi


Van: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 namens Douglas N Greve 
[gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>]
Verzonden: maandag 28 september 2015 23:58
Aan: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Onderwerp: Re: [Freesurfer] warping surface label to volume space

Something is definitely going wrong. Can you load the label as well and
verify that the label itself looks ok?

On 09/28/2015 05:32 PM, Jacobs H (NP) wrote:


Yes, here it is!
Thanks! Heidi



Yes, here it is!
Thanks! Heidi


image1.png



ATT1.txt





Op 28 sep. 2015 om 17:26 heeft Douglas N 
Greve<gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>  het 
volgende geschreven:

Can you send a picture?



On 09/28/2015 05:08 PM, Jacobs H (NP) wrote:
Dear Doug,

By looking at it in Freeview. Anatomically, I would expect that the entorhinal 
cortex would not be localized so laterally? And some voxels are not in the 
temporal lobe.

Best
Heidi


Van:freesurfer-boun...@nmr.mgh.harvard.edu<mailto:Van:freesurfer-boun...@nmr.mgh.harvard.edu>
  
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 namens Douglas N Greve 
[gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>]
Verzonden: maandag 28 september 2015 23:00
Aan:freesurfer@nmr.mgh.harvard.edu<mailto:Aan:freesurfer@nmr.mgh.harvard.edu>
Onderwerp: Re: [Freesurfer] warping surface label to volume space

how are you determining that it is not in the right place? When I run
this it works.



On 09/28/2015 04:54 PM, Jacobs H (NP) wrote:
Hi,

Bringing this to the FS list:
I am trying to warp the entorhinal cortex label (ex vivo) to volume
space, so that I can see and use the full ROI. Using the command
stated below doesnâ€™t seem to work, as it is not in the right location
of the subjectâ€™s brain. Any thoughts?

I used this command:
mri_label2vol --label S_3RSPPP/label/lh.entorhinal_exvivo.label
--regheader $SUBJECTS_DIR/S_3RSPPP/mri/orig.mgz --o
lh.entorhinal_exvivo_vol.mgz --fill-ribbon --subject S_3RSPPP --hemi l

This was the output on the terminal:
subject S_3RSPPP --hemi lh
INFO: subject not needed, igorning.
Number of labels: 1
S_3RSPPP/label/lh.entorhinal_exvivo.label
Annot File:  (null)
Template Volume: (null)
Outut Volume: lh.entorhinal_exvivo_vol.mgz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol:  1
ProjType: (null)
ProjTypeId: 0
ProjStart:  0
ProjStop: 0
ProjDelta:  0.1
Subject:  S_3RSPPP
Hemi: lh
UseNewASeg2Vol:  0
DoLabelStatVol  0
LabelCodeOffset  0
setenv SUBJECTS_DIR /autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS
$Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $
  INFO: loading
surface  
/autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/surf/lh.white

nvertices = 120130
Reading thickness
/autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/surf/lh.thickness
nlabels = 1
Loading
/autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/mri/ribbon.mgz
Loading S_3RSPPP/label/lh.entorhinal_exvivo.label
Mapping

Any suggestions how I can improve this?
Thanks
Heidi


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Re: [Freesurfer] warping surface label to volume space

2015-09-29 Thread Jacobs H (NP)

Sure, where should I upload it to?
Thanks!
Heidi

From: Douglas Greve 
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>>
Reply-To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday 29 September 2015 16:28
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] warping surface label to volume space

Can you upload the subject so I can look at it?

On 9/29/15 9:05 AM, Jacobs H (NP) wrote:

Hi Doug,

The label looks actually ok and the surface as well. I attached the images to 
this email, Not sure where it went wrong?

Best
Heidi

Van: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 namens Douglas N Greve 
[gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>]
Verzonden: maandag 28 september 2015 23:58
Aan: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Onderwerp: Re: [Freesurfer] warping surface label to volume space

Something is definitely going wrong. Can you load the label as well and
verify that the label itself looks ok?

On 09/28/2015 05:32 PM, Jacobs H (NP) wrote:

Yes, here it is!
Thanks! Heidi

Yes, here it is!
Thanks! Heidi

image1.png

ATT1.txt

Op 28 sep. 2015 om 17:26 heeft Douglas N 
Greve<gr...@nmr.mgh.harvard.edu><mailto:gr...@nmr.mgh.harvard.edu>  het 
volgende geschreven:

Can you send a picture?

On 09/28/2015 05:08 PM, Jacobs H (NP) wrote:
Dear Doug,

By looking at it in Freeview. Anatomically, I would expect that the entorhinal 
cortex would not be localized so laterally? And some voxels are not in the 
temporal lobe.

Best
Heidi

Van:freesurfer-boun...@nmr.mgh.harvard.edu<mailto:Van:freesurfer-boun...@nmr.mgh.harvard.edu>

[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 namens Douglas N Greve 
[gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>]
Verzonden: maandag 28 september 2015 23:00
Aan:freesurfer@nmr.mgh.harvard.edu<mailto:Aan:freesurfer@nmr.mgh.harvard.edu>
Onderwerp: Re: [Freesurfer] warping surface label to volume space

how are you determining that it is not in the right place? When I run
this it works.

On 09/28/2015 04:54 PM, Jacobs H (NP) wrote:
Hi,

Bringing this to the FS list:
I am trying to warp the entorhinal cortex label (ex vivo) to volume
space, so that I can see and use the full ROI. Using the command
stated below doesnâ€™t seem to work, as it is not in the right location
of the subjectâ€™s brain. Any thoughts?

I used this command:
mri_label2vol --label S_3RSPPP/label/lh.entorhinal_exvivo.label
--regheader $SUBJECTS_DIR/S_3RSPPP/mri/orig.mgz --o
lh.entorhinal_exvivo_vol.mgz --fill-ribbon --subject S_3RSPPP --hemi l

This was the output on the terminal:
subject S_3RSPPP --hemi lh
INFO: subject not needed, igorning.
Number of labels: 1
S_3RSPPP/label/lh.entorhinal_exvivo.label
Annot File:  (null)
Template Volume: (null)
Outut Volume: lh.entorhinal_exvivo_vol.mgz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol:  1
ProjType: (null)
ProjTypeId: 0
ProjStart:  0
ProjStop: 0
ProjDelta:  0.1
Subject:  S_3RSPPP
Hemi: lh
UseNewASeg2Vol:  0
DoLabelStatVol  0
LabelCodeOffset  0
setenv SUBJECTS_DIR /autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS
$Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $
  INFO: loading
surface  
/autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/surf/lh.white

nvertices = 120130
Reading thickness
/autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/surf/lh.thickness
nlabels = 1
Loading
/autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/mri/ribbon.mgz
Loading S_3RSPPP/label/lh.entorhinal_exvivo.label
Mapping

Any suggestions how I can improve this?
Thanks
Heidi

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu<mailto: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/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] warping surface label to volume space

2015-09-28 Thread Jacobs H (NP)

Hi,

Bringing this to the FS list:
I am trying to warp the entorhinal cortex label (ex vivo) to volume space, so 
that I can see and use the full ROI. Using the command stated below doesn’t 
seem to work, as it is not in the right location of the subject’s brain. Any 
thoughts?

I used this command:
mri_label2vol --label S_3RSPPP/label/lh.entorhinal_exvivo.label --regheader 
$SUBJECTS_DIR/S_3RSPPP/mri/orig.mgz --o lh.entorhinal_exvivo_vol.mgz 
--fill-ribbon --subject S_3RSPPP --hemi l

This was the output on the terminal:
subject S_3RSPPP --hemi lh
INFO: subject not needed, igorning.
Number of labels: 1
S_3RSPPP/label/lh.entorhinal_exvivo.label
Annot File:  (null)
Template Volume: (null)
Outut Volume: lh.entorhinal_exvivo_vol.mgz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol:  1
ProjType:   (null)
ProjTypeId: 0
ProjStart:  0
ProjStop:   0
ProjDelta:  0.1
Subject:  S_3RSPPP
Hemi: lh
UseNewASeg2Vol:  0
DoLabelStatVol  0
LabelCodeOffset  0
setenv SUBJECTS_DIR /autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS
$Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $
  INFO: loading surface  
/autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/surf/lh.white
nvertices = 120130
Reading thickness 
/autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/surf/lh.thickness
nlabels = 1
Loading 
/autofs/space/schopenhauer_003/users/hjacobs/SUBJECTS/S_3RSPPP/mri/ribbon.mgz
Loading S_3RSPPP/label/lh.entorhinal_exvivo.label
Mapping

Any suggestions how I can improve this?
Thanks
Heidi
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] PhD-position Research Centre Juelich

2014-08-07 Thread Jacobs H (NP)

With a staff of 4700, Forschungszentrum Jülich – a member of the Helmholtz 
Association – is one of the largest interdisciplinary research centres in 
Europe. 
Work with us on the grand challenges in the fields of health, energy  
environment, and information technology, as well as on the many and varied 
tasks of research management.
The Institute for Neuroscience and Medicine (INM) explores the structure and 
function of the brain in healthy people and in patients with neurological and 
psychiatric diseases. 
It conducts translational research with the aim to establish new procedures for 
the prevention, diagnosis and treatment of these diseases.
The Cognitive Neuroscience Division of the Institute for Neuroscience and 
Medicine (INM-3, director: Prof. G. R. Fink) cooperates closely with the 
Department of Neurology at the University Hospital of Cologne in order to 
investigate fundamental as well as clinical neuroscience questions.
For the INM-3 we are currently seeking a

Ph.D. Student (f/m)
in neuropsychology or neuroscience

Your tasks:
You will work on scientific projects focused on multi-modal longitudinal 
network mapping and modulating network breakdown in older individuals and 
patients with early Alzheimer’s disease (funded by the DFG). 
This work will be performed within the spatial cognition group and the Memory 
Clinic Köln-Jülich. 
Together with Dr. Jacobs and a team of neuropsychologists and medical doctors 
you will be trained in all research and organization aspects, ranging from data 
acquisition (neuropsychological assessments, MRI-PET scanning, cognitive and 
tDCS interventions) data analysis and writing.

Your profile:
A master’s degree neuropsychology or psychology
Experience in neuropsychological assessment
Experience with and interest in patients with cognitive deficits and 
dementia
Experience in neuroimaging ((f)MRI)
Experience with statistical analysis of data (SPSS), neuroimaging software 
packages (e.g., SPM, FSL) and programming languages (Matlab, UNIX)
Mother tongue: German
In-depth knowledge of spoken and written English
Good interpersonal skills.

Our offer:
Challenging and varied work in an interdisciplinary and international team
A wide spectrum of individual training opportunities
A three year doctorate programme including salary conforming to salary 
grade 13 of the Collective Agreement for the German Civil Service (TVöD). 

Forschungszentrum Jülich aims to employ more women in this area and therefore 
particularly welcomes applications from women. We also welcome applications 
from disabled persons.
Please submit your enquiries and application quoting the reference number 
D095/2014 to:

Dr. Heidi Jacobs, INM-3
Email: h.jac...@fz-juelich.de
Phone: (+ 49) 02461-61-3441

See als: www.fz-juelich.de



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[Freesurfer] PhD-position Research Centre Juelich

2014-08-07 Thread Jacobs H (NP)


With a staff of 4700, Forschungszentrum Jülich – a member of the Helmholtz 
Association – is one of the largest interdisciplinary research centres in 
Europe.
Work with us on the grand challenges in the fields of health, energy  
environment, and information technology, as well as on the many and varied 
tasks of research management.
The Institute for Neuroscience and Medicine (INM) explores the structure and 
function of the brain in healthy people and in patients with neurological and 
psychiatric diseases.
It conducts translational research with the aim to establish new procedures for 
the prevention, diagnosis and treatment of these diseases.
The Cognitive Neuroscience Division of the Institute for Neuroscience and 
Medicine (INM-3, director: Prof. G. R. Fink) cooperates closely with the 
Department of Neurology at the University Hospital of Cologne in order to 
investigate fundamental as well as clinical neuroscience questions.
For the INM-3 we are currently seeking a

Ph.D. Student (f/m)
in neuropsychology or neuroscience

Your tasks:
You will work on scientific projects focused on multi-modal longitudinal 
network mapping and modulating network breakdown in older individuals and 
patients with early Alzheimer’s disease (funded by the DFG).
This work will be performed within the spatial cognition group and the Memory 
Clinic Köln-Jülich.
Together with Dr. Jacobs and a team of neuropsychologists and medical doctors 
you will be trained in all research and organization aspects, ranging from data 
acquisition (neuropsychological assessments, MRI-PET scanning, cognitive and 
tDCS interventions) data analysis and writing.

Your profile:
A master’s degree neuropsychology or psychology
Experience in neuropsychological assessment
Experience with and interest in patients with cognitive deficits and 
dementia
Experience in neuroimaging ((f)MRI)
Experience with statistical analysis of data (SPSS), neuroimaging software 
packages (e.g., SPM, FSL) and programming languages (Matlab, UNIX)
Mother tongue: German
In-depth knowledge of spoken and written English
Good interpersonal skills.

Our offer:
Challenging and varied work in an interdisciplinary and international team
A wide spectrum of individual training opportunities
A three year doctorate programme including salary conforming to salary 
grade 13 of the Collective Agreement for the German Civil Service (TVöD).

Forschungszentrum Jülich aims to employ more women in this area and therefore 
particularly welcomes applications from women. We also welcome applications 
from disabled persons.
Please submit your enquiries and application quoting the reference number 
D095/2014 to:

Dr. Heidi Jacobs, INM-3
Email: h.jac...@fz-juelich.de


See als: www.fz-juelich.de



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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] 4 groups non-linear effect

2014-06-28 Thread Jacobs H (NP)



Dear FreeSurfer team,

We have processed our T1 data of 4 groups of subjects: controls and patients of 
varying degrees illness.
Now we want to perform :
- a F-test to compare the 4 groups (we have one covariate that we want to take 
into account)
- a F test to investigate a differential effect of a blood value across the 4 
groups. However, this effect might be non-linear (e.g. inverted U-shape).

We have made our fsgd-files, but now we are struggling with the contrast files.
Could you help us out on how to create these F-test contrasts?

Thanks!
Heidi



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[Freesurfer] comparing left and right cortical thickness

2013-11-22 Thread Jacobs H (NP)

Dear FreeSurfers,

Is it possible to compare left and right cortical thickness patterns, 
vertex-wise?

Thanks
Heidi



Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
h.jac...@maastrichtuniversity.nl
www.maastrichtuniversity.nl
www.heidijacobs.nl

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092

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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
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[Freesurfer] DODS slope information

2013-09-27 Thread Jacobs H (NP)

Hi Freesurfers,

I just looked at my cortical thickness results, in which I performed an 
interaction between group (2 groups) and cognition (continuous).
I see regions popping up, which is great! Especially since they are related to 
the task.
Now, I made a scatterplot of some of these vertices to get a better 
understanding of the effect. However, I am wondering how I can figure out if 
the slope within each group is significant.
How can I examine that?

Thanks!
Heidi





Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
h.jac...@maastrichtuniversity.nl
www.maastrichtuniversity.nl
www.heidijacobs.nl

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] complex repeated measure model

2013-09-24 Thread Jacobs H (NP)

Dear FreeSurfers,

I am struggling with how to set the fsgd-file and contrast file for a probably 
complex model.
I have two groups: old and young participants. For each participant, I have one 
T1-weighted image, on which I would like to perform the cortical thickness 
analyses. This T1 image was collected at baseline.
The variable of interest is cognitive performance defined on three different 
occasions (during which we applied an intervention). We want to investigate 
susceptibility for this intervention over time, as reflected in this cognitive 
outcome score.
The idea is to investigate whether susceptibility for this intervention is 
associated with different cortical thickness patterns in old versus in young 
persons.

Is there a way to capture this in one test and then do posthoc pariwise 
comparisons?

Thanks!
Heidi



Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
h.jac...@maastrichtuniversity.nl
www.maastrichtuniversity.nl
www.heidijacobs.nl

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] matrix ill-conditioned....

2013-08-28 Thread Jacobs H (NP)

Hi Doug,

Thanks! I actually thought I only had to demean variables that were not of
interest.
But this was indeed the problem, it now works!

Thank you very much!
Best
Heidi

Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
h.jac...@maastrichtuniversity.nl
www.maastrichtuniversity.nl
www.heidijacobs.nl

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092

Van: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Verzonden: dinsdag 27 augustus 2013 18:27
Aan: Jacobs H (NP)
CC: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: matrix ill-conditioned

Hi Heidi, the problem is being caused by the interaction column. Try
demeaning the ed_log and MMSE before multiplying them together to get
the interaction. Do the demeaning on the entire data set, not on a group
by group basis.
doug

On 08/27/2013 02:04 AM, Jacobs H (NP) wrote:
Sure, here it is.
Thanks
Heidi

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092

Van: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Verzonden: maandag 26 augustus 2013 23:53
Aan: Jacobs H (NP)
CC: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: matrix ill-conditioned

Can you send me the design matrix (Xg.dat) and fsgd file?

On 08/26/2013 04:35 PM, Jacobs H (NP) wrote:
Dear Doug,

Thank you. I tried to run it with this version of mri_glmfit (saved as
mri_glmfit2), but it still gives me the same error message.
I don't see the problem. I already divided the column with the interaction
by 10.
Fsgd files without MMSE and interaction factors, did not gave a problem...
Could you have a look at it? I will attach the fsgd and contrast file.

Thanks! I really appreciate your help!
Heidi

ERROR: matrix is ill-conditioned or badly scaled, condno = 101281

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
1. Your command line:
mri_glmfit2 --y
rh.Alls_educlog_MMSE_inter_agecent_ICVcent_fsgd.sm20.mgh --fsgd
/media/Data_disk/Nieuwe_map/FreeSurferOutputAD/FreeSurferOutputv450/FSGD/fsgd.Alls_educlog_MMSE_inter_agecent_ICVcent_fsgd.txt
dods --glmdir
rh.Alls_educlog_MMSE_inter_agecent_ICVcent_fsgd.dods.20.glmdir --surf
fsaverage rh --C
/media/Data_disk/Nieuwe_map/FreeSurferOutputAD/FreeSurferOutputv450/GLM_CONTRAST.MAT/contrast_3groups_Finteraction.mat
2. The FSGD file (if using one)
3. And the design matrix above

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092

Van: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Verzonden: maandag 26 augustus 2013 21:47
Aan: Jacobs H (NP)
CC: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: matrix ill-conditioned

You can try with this version of mri_glmfit which will do the rescaling
for you
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit

If the problem persists then it may be an issue with your design

doug

On 08/26/2013 01:42 PM, Jacobs H (NP) wrote:
Hi Doug,

I divided everything by 10, but the problem remains.
I have been searching a bit more. Could it be that the problem is that the
range in cognitive scores in the control group is very small?
When I run the groups separately, the patients are not a problem (the range
in cognition is very large), but the controls are still the problem.

Thanks!
Heidi

Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health

Re: [Freesurfer] matrix ill-conditioned....

2013-08-27 Thread Jacobs H (NP)

Sure, here it is.
Thanks
Heidi

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092

Van: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Verzonden: maandag 26 augustus 2013 23:53
Aan: Jacobs H (NP)
CC: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: matrix ill-conditioned

Can you send me the design matrix (Xg.dat) and fsgd file?

On 08/26/2013 04:35 PM, Jacobs H (NP) wrote:
Dear Doug,

Thank you. I tried to run it with this version of mri_glmfit (saved as
mri_glmfit2), but it still gives me the same error message.
I don't see the problem. I already divided the column with the interaction by
10.
Fsgd files without MMSE and interaction factors, did not gave a problem...
Could you have a look at it? I will attach the fsgd and contrast file.

Thanks! I really appreciate your help!
Heidi

ERROR: matrix is ill-conditioned or badly scaled, condno = 101281

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
1. Your command line:
mri_glmfit2 --y rh.Alls_educlog_MMSE_inter_agecent_ICVcent_fsgd.sm20.mgh
--fsgd
/media/Data_disk/Nieuwe_map/FreeSurferOutputAD/FreeSurferOutputv450/FSGD/fsgd.Alls_educlog_MMSE_inter_agecent_ICVcent_fsgd.txt
dods --glmdir rh.Alls_educlog_MMSE_inter_agecent_ICVcent_fsgd.dods.20.glmdir
--surf fsaverage rh --C
/media/Data_disk/Nieuwe_map/FreeSurferOutputAD/FreeSurferOutputv450/GLM_CONTRAST.MAT/contrast_3groups_Finteraction.mat
2. The FSGD file (if using one)
3. And the design matrix above

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092

Van: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Verzonden: maandag 26 augustus 2013 21:47
Aan: Jacobs H (NP)
CC: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: matrix ill-conditioned

You can try with this version of mri_glmfit which will do the rescaling
for you
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit

If the problem persists then it may be an issue with your design

doug

On 08/26/2013 01:42 PM, Jacobs H (NP) wrote:
Hi Doug,

Thanks!
Heidi

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092

Van: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Verzonden: vrijdag 23 augustus 2013 17:31
Aan: Jacobs H (NP)
CC: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] FW: FW: Contrast and F-test

The values in the interaction column are probably much larger than the
values in the other columns (thus they are badly scaled). You can
divide them by a number to bring their scale down to that of the other
columns without changing the p-values. Version 5.x does this automatically.

On 08/23/2013 11:25 AM, Jacobs H (NP) wrote:
I am using version 4.5, as all the old analyses were also done with this
version.
What do you mean with rescale?
THanks
Heidi

Van: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve

[Freesurfer] matrix ill-conditioned....

2013-08-26 Thread Jacobs H (NP)


Hi Doug,

I divided everything by 10, but the problem remains.
I have been searching a bit more. Could it be that the problem is that the 
range in cognitive scores in the control group is very small?
When I run the groups separately, the patients are not a problem (the range in 
cognition is very large), but the controls are still the problem.

Thanks!
Heidi

Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
h.jac...@maastrichtuniversity.nl
www.maastrichtuniversity.nl
www.heidijacobs.nl

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092


Van: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Verzonden: vrijdag 23 augustus 2013 17:31
Aan: Jacobs H (NP)
CC: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] FW:  FW:  Contrast and F-test

The values in the interaction column are probably much larger than the
values in the other columns (thus they are badly scaled). You can
divide them by a number to bring their scale down to that of the other
columns without changing the p-values. Version 5.x does this automatically.





On 08/23/2013 11:25 AM, Jacobs H (NP) wrote:
 I am using version 4.5, as all the old analyses were also done with this 
 version.
 What do you mean with rescale?
 THanks
 Heidi
 
 Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Verzonden: vrijdag 23 augustus 2013 17:23
 Aan: freesurfer@nmr.mgh.harvard.edu
 Onderwerp: Re: [Freesurfer] FW:  FW:  Contrast and F-test

 what version of FS are you using? It may be that you just need to
 rescale that column (if the scale is much more than the other columns)

 On 08/23/2013 11:12 AM, Jacobs H (NP) wrote:
 Hi again!

 I am trying to run these contrasts but FreeSurfer tells me that ERROR: 
 matrix is ill-conditioned or badly scaled, condno = 101380
 Possible problem with experimental design:
 Check for duplicate entries and/or lack of range of
 continuous variables within a class.

 Could this be due to the fact that there is a high correlation between 
 cognition, education and cognition x education? (the product is correlated 
 with the factors of that product)
 Or is something else going on?
 How can I solve this?

 Thanks
 Heidi

 
 Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Verzonden: donderdag 22 augustus 2013 17:52
 Aan: freesurfer@nmr.mgh.harvard.edu
 Onderwerp: Re: [Freesurfer] FW:  FW:  Contrast and F-test

 both of those contrasts are correct
 doug

 On 08/22/2013 10:51 AM, Jacobs H (NP) wrote:
 Arrghh, again wrong email, sorry

 Thanks. I think I understand the rational behind it.
 Just to be sure, would this be correct:

 For each group separately
 0 0 0 1 0 0  (group - cognition - education - cognition x education - age - 
 ICV)

 For the F-test (same order)
 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0

 Heidi


 
 Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Verzonden: donderdag 22 augustus 2013 16:46
 Aan: freesurfer@nmr.mgh.harvard.edu
 Onderwerp: Re: [Freesurfer] FW:  Contrast and F-test

 you need to have all 3. If you want to examine the interaction, then you
 need a new contrast to test the interaction. Set all to 0 except for the
 interaction term
 doug


 On 08/22/2013 10:42 AM, Jacobs H (NP) wrote:
 Dear Doug,
 Thank you for the information. Sorry for not sending this to the list.
 Do you mean that I then have to include the three variables (covariate 1, 
 covariate 2, product of these two) or only the product in the fsgd file?
 If I need to include all three of them, can you advise me on the contrasts?
 If it is only the product, I think I can use the same contrasts as before, 
 right?

 Thanks
 Heidi
 
 Dr. Heidi Jacobs
 Postdoc researcher
 Faculty of Health, Medicine and Life Sciences
 School for Mental Health and Neurosciences
 Division Cognitive Neuropsychiatry and Clinical Neurosciences
 Alzheimer Center Limburg
 h.jac...@maastrichtuniversity.nl
 www.maastrichtuniversity.nl
 www.heidijacobs.nl

 Dr. Tanslaan 12, 6229 ET Maastricht
 P.O. Box 616, 6200 MD Maastricht, The Netherlands
 T +31 43 38 84 090 F +31 43 38 84 092
 
 
 Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer

Re: [Freesurfer] matrix ill-conditioned....

2013-08-26 Thread Jacobs H (NP)

Dear Doug,

Thank you. I tried to run it with this version of mri_glmfit (saved as
mri_glmfit2), but it still gives me the same error message.
I don't see the problem. I already divided the column with the interaction by
10.
Fsgd files without MMSE and interaction factors, did not gave a problem...
Could you have a look at it? I will attach the fsgd and contrast file.

Thanks! I really appreciate your help!
Heidi

ERROR: matrix is ill-conditioned or badly scaled, condno = 101281

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
1. Your command line:
mri_glmfit2 --y rh.Alls_educlog_MMSE_inter_agecent_ICVcent_fsgd.sm20.mgh
--fsgd
/media/Data_disk/Nieuwe_map/FreeSurferOutputAD/FreeSurferOutputv450/FSGD/fsgd.Alls_educlog_MMSE_inter_agecent_ICVcent_fsgd.txt
dods --glmdir rh.Alls_educlog_MMSE_inter_agecent_ICVcent_fsgd.dods.20.glmdir
--surf fsaverage rh --C
/media/Data_disk/Nieuwe_map/FreeSurferOutputAD/FreeSurferOutputv450/GLM_CONTRAST.MAT/contrast_3groups_Finteraction.mat

2. The FSGD file (if using one)
3. And the design matrix above

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092

Van: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Verzonden: maandag 26 augustus 2013 21:47
Aan: Jacobs H (NP)
CC: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: matrix ill-conditioned

You can try with this version of mri_glmfit which will do the rescaling
for you
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit

If the problem persists then it may be an issue with your design

doug

On 08/26/2013 01:42 PM, Jacobs H (NP) wrote:
Hi Doug,

Thanks!
Heidi

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092

On 08/23/2013 11:25 AM, Jacobs H (NP) wrote:
I am using version 4.5, as all the old analyses were also done with this
version.
What do you mean with rescale?
THanks
Heidi

Van: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Verzonden: vrijdag 23 augustus 2013 17:23
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] FW: FW: Contrast and F-test

what version of FS are you using? It may be that you just need to
rescale that column (if the scale is much more than the other columns)

On 08/23/2013 11:12 AM, Jacobs H (NP) wrote:
Hi again!

I am trying to run these contrasts but FreeSurfer tells me that ERROR:
matrix is ill-conditioned or badly scaled, condno = 101380
Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.

Could this be due to the fact that there is a high correlation between
cognition, education and cognition x education? (the product is correlated
with the factors of that product)
Or is something else going on?
How can I solve this?

Thanks
Heidi

Re: [Freesurfer] FW: FW: Contrast and F-test

2013-08-24 Thread Jacobs H (NP)

Hi Doug,

I divided everything by 10, but the problem remains.
I have been searching a bit more. Could it be that the problem is that the 
range in cognitive scores in the control group is very small?
When I run the groups separately, the patients are not a problem (the range in 
cognition is very large), but the controls are still the problem.

Thanks!
Heidi

Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
h.jac...@maastrichtuniversity.nl
www.maastrichtuniversity.nl
www.heidijacobs.nl

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092


Van: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Verzonden: vrijdag 23 augustus 2013 17:31
Aan: Jacobs H (NP)
CC: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] FW:  FW:  Contrast and F-test

The values in the interaction column are probably much larger than the
values in the other columns (thus they are badly scaled). You can
divide them by a number to bring their scale down to that of the other
columns without changing the p-values. Version 5.x does this automatically.





On 08/23/2013 11:25 AM, Jacobs H (NP) wrote:
 I am using version 4.5, as all the old analyses were also done with this 
 version.
 What do you mean with rescale?
 THanks
 Heidi
 
 Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Verzonden: vrijdag 23 augustus 2013 17:23
 Aan: freesurfer@nmr.mgh.harvard.edu
 Onderwerp: Re: [Freesurfer] FW:  FW:  Contrast and F-test

 what version of FS are you using? It may be that you just need to
 rescale that column (if the scale is much more than the other columns)

 On 08/23/2013 11:12 AM, Jacobs H (NP) wrote:
 Hi again!

 I am trying to run these contrasts but FreeSurfer tells me that ERROR: 
 matrix is ill-conditioned or badly scaled, condno = 101380
 Possible problem with experimental design:
 Check for duplicate entries and/or lack of range of
 continuous variables within a class.

 Could this be due to the fact that there is a high correlation between 
 cognition, education and cognition x education? (the product is correlated 
 with the factors of that product)
 Or is something else going on?
 How can I solve this?

 Thanks
 Heidi

 
 Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Verzonden: donderdag 22 augustus 2013 17:52
 Aan: freesurfer@nmr.mgh.harvard.edu
 Onderwerp: Re: [Freesurfer] FW:  FW:  Contrast and F-test

 both of those contrasts are correct
 doug

 On 08/22/2013 10:51 AM, Jacobs H (NP) wrote:
 Arrghh, again wrong email, sorry

 Thanks. I think I understand the rational behind it.
 Just to be sure, would this be correct:

 For each group separately
 0 0 0 1 0 0  (group - cognition - education - cognition x education - age - 
 ICV)

 For the F-test (same order)
 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0

 Heidi


 
 Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Verzonden: donderdag 22 augustus 2013 16:46
 Aan: freesurfer@nmr.mgh.harvard.edu
 Onderwerp: Re: [Freesurfer] FW:  Contrast and F-test

 you need to have all 3. If you want to examine the interaction, then you
 need a new contrast to test the interaction. Set all to 0 except for the
 interaction term
 doug


 On 08/22/2013 10:42 AM, Jacobs H (NP) wrote:
 Dear Doug,
 Thank you for the information. Sorry for not sending this to the list.
 Do you mean that I then have to include the three variables (covariate 1, 
 covariate 2, product of these two) or only the product in the fsgd file?
 If I need to include all three of them, can you advise me on the contrasts?
 If it is only the product, I think I can use the same contrasts as before, 
 right?

 Thanks
 Heidi
 
 Dr. Heidi Jacobs
 Postdoc researcher
 Faculty of Health, Medicine and Life Sciences
 School for Mental Health and Neurosciences
 Division Cognitive Neuropsychiatry and Clinical Neurosciences
 Alzheimer Center Limburg
 h.jac...@maastrichtuniversity.nl
 www.maastrichtuniversity.nl
 www.heidijacobs.nl

 Dr. Tanslaan 12, 6229 ET Maastricht
 P.O. Box 616, 6200 MD Maastricht, The Netherlands
 T +31 43 38 84 090 F +31 43 38 84 092
 
 
 Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun

Re: [Freesurfer] FW: FW: Contrast and F-test

2013-08-23 Thread Jacobs H (NP)

Hi again!

I am trying to run these contrasts but FreeSurfer tells me that ERROR: matrix 
is ill-conditioned or badly scaled, condno = 101380
Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.

Could this be due to the fact that there is a high correlation between 
cognition, education and cognition x education? (the product is correlated with 
the factors of that product)
Or is something else going on?
How can I solve this?

Thanks
Heidi


Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Verzonden: donderdag 22 augustus 2013 17:52
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] FW:  FW:  Contrast and F-test

both of those contrasts are correct
doug

On 08/22/2013 10:51 AM, Jacobs H (NP) wrote:
 Arrghh, again wrong email, sorry

 Thanks. I think I understand the rational behind it.
 Just to be sure, would this be correct:

 For each group separately
 0 0 0 1 0 0  (group - cognition - education - cognition x education - age - 
 ICV)

 For the F-test (same order)
 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0

 Heidi


 
 Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Verzonden: donderdag 22 augustus 2013 16:46
 Aan: freesurfer@nmr.mgh.harvard.edu
 Onderwerp: Re: [Freesurfer] FW:  Contrast and F-test

 you need to have all 3. If you want to examine the interaction, then you
 need a new contrast to test the interaction. Set all to 0 except for the
 interaction term
 doug


 On 08/22/2013 10:42 AM, Jacobs H (NP) wrote:
 Dear Doug,
 Thank you for the information. Sorry for not sending this to the list.
 Do you mean that I then have to include the three variables (covariate 1, 
 covariate 2, product of these two) or only the product in the fsgd file?
 If I need to include all three of them, can you advise me on the contrasts?
 If it is only the product, I think I can use the same contrasts as before, 
 right?

 Thanks
 Heidi
 
 Dr. Heidi Jacobs
 Postdoc researcher
 Faculty of Health, Medicine and Life Sciences
 School for Mental Health and Neurosciences
 Division Cognitive Neuropsychiatry and Clinical Neurosciences
 Alzheimer Center Limburg
 h.jac...@maastrichtuniversity.nl
 www.maastrichtuniversity.nl
 www.heidijacobs.nl

 Dr. Tanslaan 12, 6229 ET Maastricht
 P.O. Box 616, 6200 MD Maastricht, The Netherlands
 T +31 43 38 84 090 F +31 43 38 84 092
 
 
 Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Verzonden: donderdag 22 augustus 2013 16:34
 Aan: freesurfer@nmr.mgh.harvard.edu
 Onderwerp: Re: [Freesurfer] Contrast and F-test

 If you want to test for an interaction between continuous variables,
 then you should create a new regressor by multiplying them together then
 test that regressor
 doug


 On 08/22/2013 08:09 AM, Jacobs H (NP) wrote:
 Hi all,

 I my manuscript, I examined the association between cognition and cortical 
 thickness. I first did this in three groups separately and then ran a 
 F-test.
 One of the reviewers, now wants me to examine the interaction between 
 cognition and education (all continuous).

 Would this be the correct contrast for each group separately (last two 
 zeros are for covariates, also continuous)

 0 1 -1 0 0

 Would this be the correct way for the F-test:

 0 0 0 0 0 1 -1 0 -1 1 0 0 0 0 0 0 0
 0 0 0 1 0 -1 -1 0 1 0 0 0 0 0 0

 Thanks!

 Heidi

 
 Dr. Heidi Jacobs
 Postdoc researcher
 Faculty of Health, Medicine and Life Sciences
 School for Mental Health and Neurosciences
 Division Cognitive Neuropsychiatry and Clinical Neurosciences
 Alzheimer Center Limburg
 h.jac...@maastrichtuniversity.nl
 www.maastrichtuniversity.nl
 www.heidijacobs.nl

 Dr. Tanslaan 12, 6229 ET Maastricht
 P.O. Box 616, 6200 MD Maastricht, The Netherlands
 T +31 43 38 84 090 F +31 43 38 84 092
 
 ___
 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

Re: [Freesurfer] FW: FW: Contrast and F-test

2013-08-23 Thread Jacobs H (NP)

I am using version 4.5, as all the old analyses were also done with this 
version.
What do you mean with rescale?
THanks
Heidi

Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Verzonden: vrijdag 23 augustus 2013 17:23
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] FW:  FW:  Contrast and F-test

what version of FS are you using? It may be that you just need to
rescale that column (if the scale is much more than the other columns)

On 08/23/2013 11:12 AM, Jacobs H (NP) wrote:
 Hi again!

 I am trying to run these contrasts but FreeSurfer tells me that ERROR: 
 matrix is ill-conditioned or badly scaled, condno = 101380
 Possible problem with experimental design:
 Check for duplicate entries and/or lack of range of
 continuous variables within a class.

 Could this be due to the fact that there is a high correlation between 
 cognition, education and cognition x education? (the product is correlated 
 with the factors of that product)
 Or is something else going on?
 How can I solve this?

 Thanks
 Heidi

 
 Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Verzonden: donderdag 22 augustus 2013 17:52
 Aan: freesurfer@nmr.mgh.harvard.edu
 Onderwerp: Re: [Freesurfer] FW:  FW:  Contrast and F-test

 both of those contrasts are correct
 doug

 On 08/22/2013 10:51 AM, Jacobs H (NP) wrote:
 Arrghh, again wrong email, sorry

 Thanks. I think I understand the rational behind it.
 Just to be sure, would this be correct:

 For each group separately
 0 0 0 1 0 0  (group - cognition - education - cognition x education - age - 
 ICV)

 For the F-test (same order)
 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0

 Heidi


 
 Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Verzonden: donderdag 22 augustus 2013 16:46
 Aan: freesurfer@nmr.mgh.harvard.edu
 Onderwerp: Re: [Freesurfer] FW:  Contrast and F-test

 you need to have all 3. If you want to examine the interaction, then you
 need a new contrast to test the interaction. Set all to 0 except for the
 interaction term
 doug


 On 08/22/2013 10:42 AM, Jacobs H (NP) wrote:
 Dear Doug,
 Thank you for the information. Sorry for not sending this to the list.
 Do you mean that I then have to include the three variables (covariate 1, 
 covariate 2, product of these two) or only the product in the fsgd file?
 If I need to include all three of them, can you advise me on the contrasts?
 If it is only the product, I think I can use the same contrasts as before, 
 right?

 Thanks
 Heidi
 
 Dr. Heidi Jacobs
 Postdoc researcher
 Faculty of Health, Medicine and Life Sciences
 School for Mental Health and Neurosciences
 Division Cognitive Neuropsychiatry and Clinical Neurosciences
 Alzheimer Center Limburg
 h.jac...@maastrichtuniversity.nl
 www.maastrichtuniversity.nl
 www.heidijacobs.nl

 Dr. Tanslaan 12, 6229 ET Maastricht
 P.O. Box 616, 6200 MD Maastricht, The Netherlands
 T +31 43 38 84 090 F +31 43 38 84 092
 
 
 Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Verzonden: donderdag 22 augustus 2013 16:34
 Aan: freesurfer@nmr.mgh.harvard.edu
 Onderwerp: Re: [Freesurfer] Contrast and F-test

 If you want to test for an interaction between continuous variables,
 then you should create a new regressor by multiplying them together then
 test that regressor
 doug


 On 08/22/2013 08:09 AM, Jacobs H (NP) wrote:
 Hi all,

 I my manuscript, I examined the association between cognition and cortical 
 thickness. I first did this in three groups separately and then ran a 
 F-test.
 One of the reviewers, now wants me to examine the interaction between 
 cognition and education (all continuous).

 Would this be the correct contrast for each group separately (last two 
 zeros are for covariates, also continuous)

 0 1 -1 0 0

 Would this be the correct way for the F-test:

 0 0 0 0 0 1 -1 0 -1 1 0 0 0 0 0 0 0
 0 0 0 1 0 -1 -1 0 1 0 0 0 0 0 0

 Thanks!

 Heidi

 
 Dr. Heidi Jacobs
 Postdoc researcher
 Faculty of Health, Medicine and Life Sciences
 School for Mental Health and Neurosciences
 Division Cognitive Neuropsychiatry and Clinical Neurosciences
 Alzheimer Center Limburg
 h.jac...@maastrichtuniversity.nl
 www.maastrichtuniversity.nl
 www.heidijacobs.nl

 Dr. Tanslaan 12, 6229 ET Maastricht
 P.O. Box 616, 6200 MD Maastricht, The Netherlands
 T +31 43 38 84 090 F +31 43 38 84 092

[Freesurfer] Contrast and F-test

Hi all,

I my manuscript, I examined the association between cognition and cortical 
thickness. I first did this in three groups separately and then ran a F-test.
One of the reviewers, now wants me to examine the interaction between cognition 
and education (all continuous).

Would this be the correct contrast for each group separately (last two zeros 
are for covariates, also continuous)

0 1 -1 0 0

Would this be the correct way for the F-test:

0 0 0 0 0 1 -1 0 -1 1 0 0 0 0 0 0 0
0 0 0 1 0 -1 -1 0 1 0 0 0 0 0 0

Thanks!

Heidi


Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
h.jac...@maastrichtuniversity.nl
www.maastrichtuniversity.nl
www.heidijacobs.nl

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] FW: Contrast and F-test


Dear Doug,
Thank you for the information. Sorry for not sending this to the list.
Do you mean that I then have to include the three variables (covariate 1, 
covariate 2, product of these two) or only the product in the fsgd file?
If I need to include all three of them, can you advise me on the contrasts?
If it is only the product, I think I can use the same contrasts as before, 
right?

Thanks
Heidi

Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
h.jac...@maastrichtuniversity.nl
www.maastrichtuniversity.nl
www.heidijacobs.nl

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092


Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Verzonden: donderdag 22 augustus 2013 16:34
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] Contrast and F-test

If you want to test for an interaction between continuous variables,
then you should create a new regressor by multiplying them together then
test that regressor
doug


On 08/22/2013 08:09 AM, Jacobs H (NP) wrote:
 Hi all,

 I my manuscript, I examined the association between cognition and cortical 
 thickness. I first did this in three groups separately and then ran a F-test.
 One of the reviewers, now wants me to examine the interaction between 
 cognition and education (all continuous).

 Would this be the correct contrast for each group separately (last two zeros 
 are for covariates, also continuous)

 0 1 -1 0 0

 Would this be the correct way for the F-test:

 0 0 0 0 0 1 -1 0 -1 1 0 0 0 0 0 0 0
 0 0 0 1 0 -1 -1 0 1 0 0 0 0 0 0

 Thanks!

 Heidi

 
 Dr. Heidi Jacobs
 Postdoc researcher
 Faculty of Health, Medicine and Life Sciences
 School for Mental Health and Neurosciences
 Division Cognitive Neuropsychiatry and Clinical Neurosciences
 Alzheimer Center Limburg
 h.jac...@maastrichtuniversity.nl
 www.maastrichtuniversity.nl
 www.heidijacobs.nl

 Dr. Tanslaan 12, 6229 ET Maastricht
 P.O. Box 616, 6200 MD Maastricht, The Netherlands
 T +31 43 38 84 090 F +31 43 38 84 092
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


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

[Freesurfer] FW: FW: Contrast and F-test


Arrghh, again wrong email, sorry

Thanks. I think I understand the rational behind it.
Just to be sure, would this be correct:

For each group separately
0 0 0 1 0 0  (group - cognition - education - cognition x education - age - ICV)

For the F-test (same order)
0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0

Heidi



Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Verzonden: donderdag 22 augustus 2013 16:46
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] FW:  Contrast and F-test

you need to have all 3. If you want to examine the interaction, then you
need a new contrast to test the interaction. Set all to 0 except for the
interaction term
doug


On 08/22/2013 10:42 AM, Jacobs H (NP) wrote:
 Dear Doug,
 Thank you for the information. Sorry for not sending this to the list.
 Do you mean that I then have to include the three variables (covariate 1, 
 covariate 2, product of these two) or only the product in the fsgd file?
 If I need to include all three of them, can you advise me on the contrasts?
 If it is only the product, I think I can use the same contrasts as before, 
 right?

 Thanks
 Heidi
 
 Dr. Heidi Jacobs
 Postdoc researcher
 Faculty of Health, Medicine and Life Sciences
 School for Mental Health and Neurosciences
 Division Cognitive Neuropsychiatry and Clinical Neurosciences
 Alzheimer Center Limburg
 h.jac...@maastrichtuniversity.nl
 www.maastrichtuniversity.nl
 www.heidijacobs.nl

 Dr. Tanslaan 12, 6229 ET Maastricht
 P.O. Box 616, 6200 MD Maastricht, The Netherlands
 T +31 43 38 84 090 F +31 43 38 84 092
 
 
 Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Verzonden: donderdag 22 augustus 2013 16:34
 Aan: freesurfer@nmr.mgh.harvard.edu
 Onderwerp: Re: [Freesurfer] Contrast and F-test

 If you want to test for an interaction between continuous variables,
 then you should create a new regressor by multiplying them together then
 test that regressor
 doug


 On 08/22/2013 08:09 AM, Jacobs H (NP) wrote:
 Hi all,

 I my manuscript, I examined the association between cognition and cortical 
 thickness. I first did this in three groups separately and then ran a F-test.
 One of the reviewers, now wants me to examine the interaction between 
 cognition and education (all continuous).

 Would this be the correct contrast for each group separately (last two zeros 
 are for covariates, also continuous)

 0 1 -1 0 0

 Would this be the correct way for the F-test:

 0 0 0 0 0 1 -1 0 -1 1 0 0 0 0 0 0 0
 0 0 0 1 0 -1 -1 0 1 0 0 0 0 0 0

 Thanks!

 Heidi

 
 Dr. Heidi Jacobs
 Postdoc researcher
 Faculty of Health, Medicine and Life Sciences
 School for Mental Health and Neurosciences
 Division Cognitive Neuropsychiatry and Clinical Neurosciences
 Alzheimer Center Limburg
 h.jac...@maastrichtuniversity.nl
 www.maastrichtuniversity.nl
 www.heidijacobs.nl

 Dr. Tanslaan 12, 6229 ET Maastricht
 P.O. Box 616, 6200 MD Maastricht, The Netherlands
 T +31 43 38 84 090 F +31 43 38 84 092
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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


 The information in this e-mail is intended only for the person to whom it is
 addressed. If you believe this e-mail was sent to you in error and the e-mail
 contains patient information, please contact the Partners Compliance HelpLine 
 at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.


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



--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] FW: FW: Contrast and F-test

Great!! Thank you so much!
Heidi

Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
h.jac...@maastrichtuniversity.nl
www.maastrichtuniversity.nl
www.heidijacobs.nl

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092


Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Verzonden: donderdag 22 augustus 2013 17:52
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] FW:  FW:  Contrast and F-test

both of those contrasts are correct
doug

On 08/22/2013 10:51 AM, Jacobs H (NP) wrote:
 Arrghh, again wrong email, sorry

 Thanks. I think I understand the rational behind it.
 Just to be sure, would this be correct:

 For each group separately
 0 0 0 1 0 0  (group - cognition - education - cognition x education - age - 
 ICV)

 For the F-test (same order)
 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0
 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0

 Heidi


 
 Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Verzonden: donderdag 22 augustus 2013 16:46
 Aan: freesurfer@nmr.mgh.harvard.edu
 Onderwerp: Re: [Freesurfer] FW:  Contrast and F-test

 you need to have all 3. If you want to examine the interaction, then you
 need a new contrast to test the interaction. Set all to 0 except for the
 interaction term
 doug


 On 08/22/2013 10:42 AM, Jacobs H (NP) wrote:
 Dear Doug,
 Thank you for the information. Sorry for not sending this to the list.
 Do you mean that I then have to include the three variables (covariate 1, 
 covariate 2, product of these two) or only the product in the fsgd file?
 If I need to include all three of them, can you advise me on the contrasts?
 If it is only the product, I think I can use the same contrasts as before, 
 right?

 Thanks
 Heidi
 
 Dr. Heidi Jacobs
 Postdoc researcher
 Faculty of Health, Medicine and Life Sciences
 School for Mental Health and Neurosciences
 Division Cognitive Neuropsychiatry and Clinical Neurosciences
 Alzheimer Center Limburg
 h.jac...@maastrichtuniversity.nl
 www.maastrichtuniversity.nl
 www.heidijacobs.nl

 Dr. Tanslaan 12, 6229 ET Maastricht
 P.O. Box 616, 6200 MD Maastricht, The Netherlands
 T +31 43 38 84 090 F +31 43 38 84 092
 
 
 Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Verzonden: donderdag 22 augustus 2013 16:34
 Aan: freesurfer@nmr.mgh.harvard.edu
 Onderwerp: Re: [Freesurfer] Contrast and F-test

 If you want to test for an interaction between continuous variables,
 then you should create a new regressor by multiplying them together then
 test that regressor
 doug


 On 08/22/2013 08:09 AM, Jacobs H (NP) wrote:
 Hi all,

 I my manuscript, I examined the association between cognition and cortical 
 thickness. I first did this in three groups separately and then ran a 
 F-test.
 One of the reviewers, now wants me to examine the interaction between 
 cognition and education (all continuous).

 Would this be the correct contrast for each group separately (last two 
 zeros are for covariates, also continuous)

 0 1 -1 0 0

 Would this be the correct way for the F-test:

 0 0 0 0 0 1 -1 0 -1 1 0 0 0 0 0 0 0
 0 0 0 1 0 -1 -1 0 1 0 0 0 0 0 0

 Thanks!

 Heidi

 
 Dr. Heidi Jacobs
 Postdoc researcher
 Faculty of Health, Medicine and Life Sciences
 School for Mental Health and Neurosciences
 Division Cognitive Neuropsychiatry and Clinical Neurosciences
 Alzheimer Center Limburg
 h.jac...@maastrichtuniversity.nl
 www.maastrichtuniversity.nl
 www.heidijacobs.nl

 Dr. Tanslaan 12, 6229 ET Maastricht
 P.O. Box 616, 6200 MD Maastricht, The Netherlands
 T +31 43 38 84 090 F +31 43 38 84 092
 
 ___
 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

[Freesurfer] Contrast of three groups

2013-05-29 Thread Jacobs H (NP)

Hi FreeSurfers,

I have a more statistical question:

I have three groups of subjects and I want to examine the effect of a 
continuous variable (cognition). Is it possible to examine three groups? Or 
should I do pairwise comparisons?
What would the contrast than look like? Something like this:

0 0 0 0 0 0 0.33 0.33 0.33

(first three zeros for the three groups; three zeros for age-correction; three 
weights for cognition scores)??

Thanks!

Heidi



Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
h.jac...@maastrichtuniversity.nl
www.maastrichtuniversity.nl
www.heidijacobs.nl

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Contrast of three groups

2013-05-29 Thread Jacobs H (NP)

Hi Doug,

Thanks for the answer. How can I examine differences between the groups?

Best
Heidi


Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Verzonden: woensdag 29 mei 2013 17:30
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] Contrast of three groups

Hi Heidi, That will test the effect of the continuous variable averaged
over the 3 groups.
doug


On 05/29/2013 10:40 AM, Jacobs H (NP) wrote:
 Hi FreeSurfers,

 I have a more statistical question:

 I have three groups of subjects and I want to examine the effect of a 
 continuous variable (cognition). Is it possible to examine three groups? Or 
 should I do pairwise comparisons?
 What would the contrast than look like? Something like this:

 0 0 0 0 0 0 0.33 0.33 0.33

 (first three zeros for the three groups; three zeros for age-correction; 
 three weights for cognition scores)??

 Thanks!

 Heidi


 
 Dr. Heidi Jacobs
 Postdoc researcher
 Faculty of Health, Medicine and Life Sciences
 School for Mental Health and Neurosciences
 Division Cognitive Neuropsychiatry and Clinical Neurosciences
 Alzheimer Center Limburg
 h.jac...@maastrichtuniversity.nl
 www.maastrichtuniversity.nl
 www.heidijacobs.nl

 Dr. Tanslaan 12, 6229 ET Maastricht
 P.O. Box 616, 6200 MD Maastricht, The Netherlands
 T +31 43 38 84 090 F +31 43 38 84 092
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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The information in this e-mail is intended only for the person to whom it is
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[Freesurfer] warping results on surface

2013-02-12 Thread Jacobs H (NP)

Hi FreeSurfer!

A colleague has retinotopic results that he would like to overlay on the FS 
surface (most likely fsaverage).
The retinotopic data is in 2mm isotropic resolution.
What would be the best way to be able to overlay this data correctly?
Should he first warp the volume to the volume of fsaverage and then use 
vol2surf?

Any help is highly appreciated!

Best
Heidi



Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
h.jac...@maastrichtuniversity.nl
www.maastrichtuniversity.nl
www.heidijacobs.nl

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] basic comparison

Hi FreeSurfers,

I am preparing a simple presentation, to show some basic stuff in my lab and 
therefore I would like to compare the cortical thickness of two subjects.
Is there a way to do this? For the GLM, I probably have not enough degrees of 
freedom? Is there a way that I could subtract the two thickness overlays?

Thanks
Heidi


Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
h.jac...@maastrichtuniversity.nl
www.maastrichtuniversity.nl
www.heidijacobs.nl

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] basic comparison

Hi Doug,

Thanks for your help. I just ran the mri_glmfit the way you suggested. But 
FreeSurfer does not provide me a contrast directory and no gamma.mgh. It only 
gives me a mask.mgh, Xg.dat and the mri_glmfit.log?

Any ideas what might have gone wrong?

Thanks!
Heidi

Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
h.jac...@maastrichtuniversity.nl
www.maastrichtuniversity.nl
www.heidijacobs.nl

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092


Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Verzonden: donderdag 11 oktober 2012 17:35
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] basic comparison

Hi Heidi, the easiest way is probably to do the analysis with mri_glmfit
specifying that each subject is it's own group and a contrast to compute
the difference between the groups.The gamma.mgh in the contrast
directory will be the thickness difference between the two subjects.
There will be a sig.mgh there as well, but, as you mention, you will not
be able to get reasonable p-values out because of not enough DOF.
doug

On 10/11/2012 08:31 AM, Jacobs H (NP) wrote:
 Hi FreeSurfers,

 I am preparing a simple presentation, to show some basic stuff in my lab and 
 therefore I would like to compare the cortical thickness of two subjects.
 Is there a way to do this? For the GLM, I probably have not enough degrees of 
 freedom? Is there a way that I could subtract the two thickness overlays?

 Thanks
 Heidi

 
 Dr. Heidi Jacobs
 Postdoc researcher
 Faculty of Health, Medicine and Life Sciences
 School for Mental Health and Neurosciences
 Division Cognitive Neuropsychiatry and Clinical Neurosciences
 Alzheimer Center Limburg
 h.jac...@maastrichtuniversity.nl
 www.maastrichtuniversity.nl
 www.heidijacobs.nl

 Dr. Tanslaan 12, 6229 ET Maastricht
 P.O. Box 616, 6200 MD Maastricht, The Netherlands
 T +31 43 38 84 090 F +31 43 38 84 092
 
 ___
 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] basic comparison

Hi Doug,

This is from the log file: 


mri_glmfit --y lh.Hybridversustrio_fsgd.sm20.mgh --fsgd 
/Volumes/HEIDI2/comparingTrioHybrid/FSGD/fsgd.Hybridversustrio_fsgd.txt dods 
--glmdir lh.Hybridversustrio_fsgd.dods.20.glmdir --surf fsaverage lh --C 
/Volumes/HEIDI2/comparingTrioHybrid/GLM_CONTRAST.MAT/contrast_1_-1.mat 
sysname  Darwin
hostname medmac47.ime.kfa-juelich.de
machine  x86_64
user hjacobs
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/Volumes/HEIDI2/comparingTrioHybrid/THICKNESS_GLM/lh.Hybridversustrio_fsgd.sm20.mgh
logyflag 0
usedti  0
FSGD /Volumes/HEIDI2/comparingTrioHybrid/FSGD/fsgd.Hybridversustrio_fsgd.txt
labelmask  /Volumes/HEIDI2/comparingTrioHybrid/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.Hybridversustrio_fsgd.dods.20.glmdir
IllCondOK 0
DoFFx 0

Heidi



Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
h.jac...@maastrichtuniversity.nl
www.maastrichtuniversity.nl
www.heidijacobs.nl

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092


Van: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Verzonden: donderdag 11 oktober 2012 17:52
Aan: Jacobs H (NP)
CC: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] basic comparison

what's your command line and resulting terminal output?

On 10/11/2012 11:49 AM, Jacobs H (NP) wrote:
 Hi Doug,

 Thanks for your help. I just ran the mri_glmfit the way you suggested. But 
 FreeSurfer does not provide me a contrast directory and no gamma.mgh. It only 
 gives me a mask.mgh, Xg.dat and the mri_glmfit.log?

 Any ideas what might have gone wrong?

 Thanks!
 Heidi
 
 Dr. Heidi Jacobs
 Postdoc researcher
 Faculty of Health, Medicine and Life Sciences
 School for Mental Health and Neurosciences
 Division Cognitive Neuropsychiatry and Clinical Neurosciences
 Alzheimer Center Limburg
 h.jac...@maastrichtuniversity.nl
 www.maastrichtuniversity.nl
 www.heidijacobs.nl

 Dr. Tanslaan 12, 6229 ET Maastricht
 P.O. Box 616, 6200 MD Maastricht, The Netherlands
 T +31 43 38 84 090 F +31 43 38 84 092
 
 
 Van: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
 [gr...@nmr.mgh.harvard.edu]
 Verzonden: donderdag 11 oktober 2012 17:35
 Aan: freesurfer@nmr.mgh.harvard.edu
 Onderwerp: Re: [Freesurfer] basic comparison

 Hi Heidi, the easiest way is probably to do the analysis with mri_glmfit
 specifying that each subject is it's own group and a contrast to compute
 the difference between the groups.The gamma.mgh in the contrast
 directory will be the thickness difference between the two subjects.
 There will be a sig.mgh there as well, but, as you mention, you will not
 be able to get reasonable p-values out because of not enough DOF.
 doug

 On 10/11/2012 08:31 AM, Jacobs H (NP) wrote:
 Hi FreeSurfers,

 I am preparing a simple presentation, to show some basic stuff in my lab and 
 therefore I would like to compare the cortical thickness of two subjects.
 Is there a way to do this? For the GLM, I probably have not enough degrees 
 of freedom? Is there a way that I could subtract the two thickness overlays?

 Thanks
 Heidi

 
 Dr. Heidi Jacobs
 Postdoc researcher
 Faculty of Health, Medicine and Life Sciences
 School for Mental Health and Neurosciences
 Division Cognitive Neuropsychiatry and Clinical Neurosciences
 Alzheimer Center Limburg
 h.jac...@maastrichtuniversity.nl
 www.maastrichtuniversity.nl
 www.heidijacobs.nl

 Dr. Tanslaan 12, 6229 ET Maastricht
 P.O. Box 616, 6200 MD Maastricht, The Netherlands
 T +31 43 38 84 090 F +31 43 38 84 092
 
 ___
 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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


 The information in this e-mail is intended only for the person to whom it is
 addressed. If you believe this e-mail was sent to you in error and the e-mail
 contains patient information, please contact the Partners Compliance HelpLine 
 at
 http://www.partners.org

Re: [Freesurfer] basic comparison